A document by Zu jiao Shi, written on Authorea.

Spatially explicit coalescent models in which the underlying demographic parameters are informed by the environment (either past, present, or temporally and spatially changing environments) provide a framework for hypothesis testing that incorporates geographic information about genetically sampled individuals. This general approach - Integrated Distributional, Demographic and Coalescent (iDDC) modelling - can be used to explain how heterogeneous, dynamic landscapes shape the history and genetic patterns of a species. However, iDDC approaches involve long and complex tasks that often require custom-fit simulators, some coding expertise, and extensive computing resources. Here we introduce several resources that offer improved speed and generality, as well as expand the feasible parameter space for conducting iDDC analyses compared to other software applications. Specifically, QUETZAL-EGGS are C++ iDDC simulators; QUETZAL-CRUMBS is a complementary set of Python tools for simulating on specific landscapes and conducting Approximate Bayesian Computation (ABC) analyses (e.g., prior sampling, geospatial operations, ENM/SDM, visualization); DECRYPT is a framework for automated, biology-informed robustness analysis of the multispecies coalescent model. All these tools and their dependencies for local use or remote computations are made readily available in a Docker container package called QUETZAL-NEST.

The assessment of soil erosion rate, especially in agricultural lands, represents a fundamental tool for land management planning in the long-term period. In this study, the SWAT model was utilized to simulate soil erosion within a semi-arid watershed in South Portugal. The model was successfully calibrated and validated using real data of streamflow and river sediment transport in four hydrometric stations. Soil erosion susceptibility maps (historical and future) were realized to highlight the evolution of the phenomenon through time. The historical period was confirmed to be the worst one in terms of average soil erosion for each land use, followed by the Representative Concentration Pathways (RCPs) 8.5 and 4.5 scenarios. The main differences in soil loss among the two RCPs will be influenced by the slightly increasing trend of extreme events which will characterize the RCP 8.5, leading to a higher maximum value of soil erosion. Results highlighted the tendency to erosion of Leptosols and of the agro-forestry system (“montado”), which influenced the soil erosion susceptibility distribution of the whole basin. The study confirmed that Leptosols are the most subject to sediment loss due to their intrinsic characteristics, and that “montado” and farmed systems will negatively influence soil erosion rate if anti-erosion actions will not be adopted, stressing the need to identify all aspects responsible for land degradation in Mediterranean watersheds.

Abstract Objective: To determine the occurrence of sporadic and periodic accelerations during labour and odds ratio, OR, for acidaemia. Design: Case-control study. Setting: One regional and one university hospital. Sample: Cardiotocograms, CTGs, from 295 neonates with cord blood pH <7.05 born during the second stage of labour, 70 neonates with cord blood pH <7.10 born during the first stage and 731 controls with pH ≥7.15. Method: The last 30-60 minutes of CTG recordings before birth from 365 neonates born with acidaemia and from the corresponding stage in labour for 731 controls were scrutinized. Main outcome measures: Odds ratio with 95% confidence interval for acidaemia at birth. Results: During the first stage, sporadic accelerations were present in 16% of cases and 78% of controls; OR for acidaemia 0.05 (0.02-0.10). In the second stage the corresponding rates were 13% and 60%; OR 0.09 (0.06-0.14). Isolated periodic accelerations were infrequent. A weak negative association with acidaemia was found in the second stage; OR 0.51 (0.30-0.86), whereas it was not significant in the first stage; OR 0.24 (0.04-1.4). Less than two sporadic accelerations were associated with an increased risk of acidaemia despite normal fetal heart rate variability (5-25 beats per minute, OR 10.3 (7.2-14.8)). Conclusions: Sporadic accelerations indicate a very low probability of acidosis but are absent in 40% of fetuses with normal pH during a 30-60 minutes second stage recording. Tweetable abstract: Sporadic, but not periodic, accelerations indicate normal fetal pH. This should be a part of CTG guidelines.

Choroideremia (CHM), is caused by a defect on the X gene which prohibits the body from making RAB Escort Protein-1, or REP-1, which further lead vision lost. The biological role of RAB Escort Protein-1 (REP-1) determine by homology modeling. In this research work the structure of Rab11 was predicted using Geno3d server. Ramachandran plot obtained by Geno 3-D server to estimate the effect of amino acid. The predicted structure was visualized through different visualization tools such as Pymol, Rasmol, and Swiss-pdb viewer. The active site was predicted through Q-site finder for further drug discovery and development for said disease.

Half of the world’s livestock live in (semi-)arid regions, where an important proportion of the population relies on animal husbandry for survival. However, overgrazing can lead to land degradation and subsequent socio-economic crises. Sustainable management of dry rangeland requires suitable stocking strategies and has been the subject of intense debate in the last decades. Our goal is to understand how variations in stocking strategies affect the resilience of dry rangelands. We describe the rangeland dynamics through a simple mathematical model consisting of a system of coupled differential equations. We assume that the livestock density is limited by forage availability only, which is itself limited by water availability. We model processes typical of dryland vegetation as a strong Allee effect, leading to bistability between a vegetated and a degraded state, even in the absence of herbivores. We study analytically the impact of varying the stocking density and the destocking adaptivity on the resilience of system to the effects of drought. By using dynamical systems theory, we look at how different measures of resilience are affected by variations in strategies. We find that: 1)Increasing the stocking density decreases the resilience, giving rise to an expected trade-off between productivity and resilience. 2)There exists a maximal sustainable livestock density above which the system can only be degraded. This animals carrying capacity is common to all strategies. 3) Higher adaptivity of the destocking rate to available forage makes the system more resilient: the more adaptive a system is, the bigger the losses of vegetation it can recover from, without affecting the long term level of productivity. The first two results emphasize the need for adapted dry rangeland management strategies, in order to prevent degradation resulting from the conflict between profitability and sustainability. The third point offers a theoretical suggestion for such a strategy.

Conventional mesh-based numerical methodologies cannot accurately simulate high-speed impact welding due to extreme distortion of mesh. Therefore, a smoothed particle hydrodynamics (SPH) based methodology is implemented to study the welding morphology and jetting phenomenon during magnetic pulse welding (MPW) of D9 clad tubes and  SS 316LN end plugs after carrying out electromagnetic and structural deformation analysis using Lagrangian Finite element method. Different experimental parameters like taper angle, taper length, stand-off distance and discharge energies are varied to minimise leak-tightness. Discharge voltage of 17 kV and 18 kV and taper angle of 8 degrees is observed to be best suited during the experiment. Simulation results are validated with experimental observations. Furthermore, the joints are tested with the help of various non-destructive and destructive techniques. Uniformity at the joint interface is established by X-ray computer tomography. Moreover, the hydraulic pressure burst test shows failure in the unwelded region at the burst pressure of 105 MPa. Therefore, the current work discusses the applicability of the MPW technique as an alternative method to create a D9 tube to SS 316 LN end plug for a fast breeder reactor and the SPH technique on successfully reproducing experimentally observed interface morphology.

Clinician bias on the low resource workfloorThis is a mini commentary on R Goldenberg et al.,In this study in two LMIC settings in Asia, expert panels who looked at cause of death of premature neonates, with significantly more information available, found far more birth asphyxia and less Respiratory Distress Syndrome than the discharging NICU physicians did. Some NICU physicians attributed respiratory distress in the premature neonate to RDS by default, especially if there was no other information to contradict this belief. Especially in the Pakistan setting, birth asphyxia did not seem to be on the mind of the physician.What could be possible explanations?The maternal population, illiteracy rates, low rates of NICU admission and high death rates in the Pakistan setting suggest an impoverished background population and very restrained resources.In such setting one could easily imagine diagnostic means and treatment options are limited. If there is also lack of staff, reduced availability of beds, and work overload (ref: authors correspondence), priorities have to be made who to admit and who to treat. Life expectancy and quality of life may play a role in triaging.Physicians who work in labourward settings without CTGs may recognize the viewpoint that obstetric management only be guided by the maternal condition. On several SubSaharan African labourwards I experienced that decisions were not (solely) to be based on the supposed fetal condition. To perform ‘an unnecessary caesarean section’, or on the other hand to try and salvage the life of a baby who then turns out to be brain damaged after a poor start, was not seen as good obstetric care. A premature baby with apparent severe birth asphyxia might consequently not be transferred to the NICU. A baby who is admitted may not carry the diagnosis birth asphyxia since, as the authors point out this may imply mismanagement. It could even go further: if potential fetal compromise is not relevant in the obstetric management, it may also not be picked up. The obstetric physician could in such situation easily develop a blind spot for birth asphyxia.Another cause of clinician bias in such low resource settings could be underestimation of the gestation, making RDS a more likely diagnosis. If gestational scans are not available, and last menstrual periods are unreliable (associated with illiteracy) gestational age is more often estimated by fundal height at presentation in labourward, or by the birthweight of the baby. Underestimation could be the case in Pakistan where 65% of babies were thought to be less than 32 weeks, only 12,5 % of the neonates were thought to be growth restricted which is associated with birth asphyxia, but nearly 63 % suffered with birth asphyxia according to the panel.These are several hypotheses how physicians in a low resource setting could form biases in their clinical thinking, which, when not corrected by other information, could lead to incorrect diagnoses and mismanagement. This correcting information could come from diagnostic tools, such as PCR tests Xchest, etc,. However, sufficient time and systems in place for proper handovers, e.g. between the obstetrician and pediatrician, an open mind and awareness of pitfalls, audit and reflection on one’s management, and training to stay up to date are just as important. Hopefully expert panel studies such as these, could stimulate awareness and be a motor to improved Obstetric and Pediatric Care in LMIC settings.

Daily light-dark cycles shape the physiology and activity patterns of nearly all organisms. Recent evidence that gut microbial oscillations synchronise circadian rhythms in host immunity and metabolism indicate that diurnal dynamics is a crucial component of microbiome function. However, their prevalence and functional significance are rarely tested in natural populations. Here we summarize the hallmarks of gut microbiota rhythms and outline the mechanisms by which they synchronise rhythms in host immunity and metabolism. We discuss the consequences for diverse biological processes such as host pathogen susceptibility and seasonal switches in metabolism, and discuss how the breakdown of these circadian interactions, for example during senescence and as a consequence of urbanisation, may affect wildlife infection risk and disease. Lastly, we provide practical guidelines for the measurement of microbial oscillations in wildlife, highlighting that whilst wild animals are rarely available over a 24-hour period, characterising even parts of the cycle can be informative. Light-dark cycles are an almost universal environmental cue and provide a rare opportunity to generalise gut microbial responses across species. A better understanding of how microbial rhythms manifest in wildlife is required to fully comprehend their ecological significance.

To assess the association between single, isolated left SVC and coarctation of the aorta. Retrospective review Fetal cardiac centre in London, split across two sites. 24001 fetal cardiac scans performed between April 2005 and March 2020, of which 24 fetuses were found to have isolated single left SVC. Retrospective analysis of clinical reports and outcome data were examined from routinely captured clinical data; this data was compared to gestation-matched references. Presence of aortic arch hypoplasia and/or coarctation of the aorta. 289 fetuses were identified with left SVC, of those 24 (8.3%) had single left SVC with agenesis of the right SVC. 95.8% (23/24) were identified after the introduction of the 3VV to the fetal anomaly screening programme in 2010 of which 58.35 (14/24) were diagnoses after the addition of the 3VT in 2015. All fetuses were successfully delivered without any postnatal complications. None were found to have aortic arch hypoplasia or coarctation of the aorta. Single LSVC does not appear to be associated with CoA and can be considered a benign congenital anomaly. Changes in streaming of flow across the patent foramen ovale, thus maintaining adequate perfusion of the aortic isthmus in fetal life, may be the reasons for not developing coarctation of the aorta. Furthermore, frequency of antenatal scans can be minimized, and postnatal management adjusted accordingly as single LSVC in the absence of right SVC does not appear to result in development of coarctation of the aorta, neither antenatally nor after birth.

Objective: To evaluate patient and clinician views regarding Patient-Initiated Follow-Up (PIFU) in gynaecology and identify subgroups suited to this pathway of care. Design: Cross-sectional survey Setting: Gynaecology Outpatients Department, Sheffield Teaching Hospitals, Sheffield, UK. Population or Sample: Patients and clinicians. Methods: Participants were recruited from gynaecology outpatients, with purposive sampling of diverse groups and clinics. PIFU value and burden were evaluated using patient and clinician surveys (modified QQ-10). Free-text comments were collated. Main Outcome Measures: QQ-10 value and burden scores. Results: 305 patients and 30 clinicians were surveyed. On value and burden scales of 0–100, patients and clinicians attributed high value (mean 77 and 81) and low burden (mean 38 and 45). Greater autonomy was cited in free-text by 85% of patients and 93% of clinicians. Patients attending benign gynaecological sub-specialties attributed highest mean value scores: Endometriosis (84), general gynaecology (83) and vulval clinics (81). Gynaecology oncology patients attributed lowest value (64) and highest burden (51) of all subgroups. Younger patients (<60) were more likely to express preference for PIFU (53%) than older (29%). Conclusions: Patients and clinicians are in favour of selected use of PIFU in Gynaecology. Both surveys found younger patients with benign gynaecological conditions well-suited to PIFU. We recommend offering PIFU to select patients confident in self-monitoring, whilst respecting patient choice so patients are not disadvantaged by this system. Further evaluation of PIFU in women’s health is warranted, including more detailed socio-economic and outcomes assessment. Funding: None Keywords: Patient-Initiated Follow-Up, Women’s Health, Gynaecology, Survey, Self-Monitoring

Primary cardiac angiosarcomas are rare tumors. Here, we report a case of primary cardiac angiosarcoma originating in the left atrium. The tumor resulted in mitral stenosis with regurgitation, tricuspid regurgitation, and severe pulmonary hypertension. After admission, the tumor was surgically removed. During the operation, it was found that the tumor originated from the mitral valve and invaded the valve annulus. How to place the artificial valve after the tumor was removed is the key to the success of the surgery. In this article, we aim to provide insights into the diagnosis, symptoms, and manifestations of primary cardiac angiosarcoma, as well as an alternative approach to intraoperative annulus reconstruction, and emphasize the importance of early diagnosis, treatment, and positive prognosis.

The reported case is a 53-year-old woman with the history of long-standing rheumatoid arthritis who first presented with acute-onset dizziness and gait disturbance, periventricular linear and radial enhancement pattern on MRI and normal CSF analysis, successfully treated with an increase in the dose of oral steroids.

Monochorionic twins (MC) are at increased risk of CHDs, especially acquired CHDs in twin-twin transfusion syndrome (TTTS). Multiple cardiac abnormalities in MC twins with TTTS are to be expected due to cardiac hemodynamic changes. Therefore, more attention to this group of patients should be given regarding heart abnormalities.

We report the clinical, imaging, echocardiography and muscle biopsy findings of a patient presenting by characteristics which have not been reported in previous Melas cases. This is the first reported case of MELAS accompanying with PFO, and the first case of MELAS with the progressive pattern of ischemic lesions.

In plasmid DNA (pDNA) production from Gram-negative bacteria, endotoxin has been known as the major contaminant. The separation becomes difficult due to its ability to form a stable complex with pDNA apart from sharing common properties like surface charge, molecular size, temperature and pH stability. This study focused on the analysis of zeta potential of endotoxin, theoretical number of cation bound per molecule of endotoxin as well as binding tendency of cations towards endotoxin in the presence of pDNA. These analyses were conducted under various experimental conditions such as types of divalent metal cation, cation concentration, pH and incubation time. The analysis of zeta potential at different cation concentrations and pH values showed that Mg2+ had the most significant effect on endotoxin surface charge. The zeta potential of endotoxin reduced by a magnitude of 43.55 mV, from -43.53 mV to 0.02 mV in the presence of 2.0 M Mg2+, and a magnitude of 44.12 mV , from -43.53 mV to 0.59 mV at the lowest pH level. However, in the analysis of theoretical number of cation bound per molecule of endotoxin, Zn2+ showed the highest number (0.6) compared to Ca2+ (0.12) and Mg2+ (0.05). The tendency of Zn2+ to preferentially bind with endotoxins forming larger aggregated structure was also evident in the DNA gel electrophoresis and transmission electron microscopic analysis.

By a discrete space , we mean here a collection of finite or a countable infinite number of vertices which has a graph structure provided by a set of edges (finite or countable infinite in number). In many cases, the varying graph structures (connectivity type problems) are themselves very interesting and important. However, there are some important examples where the study of the intricate role of functions on is essential (example: potential functions, effective resistance, Kirchhoff problem in electrical networks; and escape probability, Dirichlet functions, hitting time in random walks). In this survey article we review a part of the function theory developed by some researchers in this field and present a cohesive narrative. We have placed special emphasis on different discrete versions of the Dirichlet problem, the Neumann problem and the Poisson equation.

Objective: To analyse perceived barriers to access to formal abortion services and the demand for medical abortion in Turkey Design: Mixed-method study Population sample: Pregnant women in Turkey who filled the consultation survey on Women on Web website between 1 January 2013 and 12 October 2020 Method: Our dataset includes anonymized responses of 620 women to the online consultation survey and anonymized email correspondences of 138 women with the WoW help desk. We conducted a cross-sectional analysis of the survey data and a content analysis of email correspondences. Main outcome measures: Perceived barriers to formal abortion services in Turkey Results: The surveyors listed various reasons for requesting an abortion; while 59.68% of them mentioned that they just cannot have a child at this point, financial constraints (49.84%), wanting to finish school (31.77%) and being too young (31.29%) were among the leading reasons. Several barriers to access to formal abortion services were reported; the most frequently cited barriers include cost (48.31%), the need to keep abortion secret from partner or family (42.69%) and unavailability of abortion pills (44.94%). Our qualitative analysis of women’s email correspondences has demonstrated some additional barriers to and concerns over the formal abortion services. These include censorship of abortion information and misinformation, denial of care, concerns over spousal consent, cost, abortion method, trust, and confidentiality. Conclusions: We conclude that despite the legal framework, abortion remains difficult to access and approach for women in Turkey due to legal barriers and concerns over formal abortion services.

Background Childhood cancer survivors face late health problems; despite advances in research, details on risk remain unclear. We describe the methodological aspects of the Dutch Childhood Cancer Survivor Study (DCCSS) cross-sectional clinical study (LATER 2 study). Procedure From the multi-center DCCSS LATER cohort of 6,165 five-year survivors diagnosed 1963-2001, we invited 4,735 eligible in 2016, as well as siblings and parents of survivors. Gaps in evidence identified during development of surveillance guidelines were translated into clinical research questions for 16 outcome-specific sub-projects. The regular care visit to the LATER outpatient clinic forms the backbone of outcome assessment complemented with research-defined measurements (physical examination, diagnostic tests, questionnaires). Furthermore, blood/saliva samples were taken for DNA extraction. Results In total, 2519 (53.2%) survivors participated in the LATER 2 study. Of those participating survivors, 49.3% was female. Median time since childhood cancer diagnosis was 26.9 years (range 14.8 to 54.7 years) and median attained age was 34.4 years (range 15.4 to 66.6 years). Conclusions The high-quality data generated in the LATER 2 study will provide valuable insights into risks of and risk factors for clinical and (psychosocial) health outcomes and factors for early recognition of (psychosocial) health outcomes in long-term childhood cancer survivors. This will contribute to fill in important gaps in knowledge and improve the quality of life and care for childhood cancer survivors.

Objective: We previously described a technique for repair of the myometrial defect at repeat Caesarean section which increases residual myometrial thickness thereby potentially reducing future niche-related complications. Here we describe how this technique can be modified for use for placenta accreta spectrum disorders. Design: Comparison of surgical performance of the modified technique with peripartum hysterectomy in women having repeat Caesarean delivery for placenta accreta Setting: A two year retrospective case control study at a tertiary unit in Singapore. Population: All women with placenta accreta spectrum disorder between December 2019 and October 2021. Methods: After delivery through the isthmocele women either underwent the modified technique which comprised uterine exteriorisation, systematic placental removal initiated from the posterior uterine wall, identification, mobilization and apposition of the boundaries of myometrial defects and repair or peripartum hysterectomy. Main Outcome Measures: Operating time, estimated blood loss and complication rate. Results: Ten women had Caesarean hysterectomy and ten had Caesarean section using the modified approach. Age and gestational age at delivery were similar for the two groups. Women in the modified technique group had had fewer prior Caesarean sections and had a lower body mass index. Operating time, estimated blood loss and need for transfusion were lower in the myometrial repair group but without statistical significance and there were no visceral injuries. There was one bladder injury in the hysterectomy group. Conclusion: The modified approach provides an effective alternative to peripartum hysterectomy with favourable surgical profile and allows uterine conservation with restoration of myometrial thickness.

Parasites form an integral part of food webs, however, mechanistic insights into the role of parasites for energy flow and community dynamics is currently limited by a lack of conceptual studies investigating host-parasite interactions in a community context. In aquatic systems, chytrids constitute a major group of fungal parasites and their free-living infective stage (zoospores) forms a highly nutritional food source to zooplankton. Consumption of zoospores can create an energy pathway from otherwise inedible phytoplankton to zooplankton (“mycoloop”). The impact of such parasite-mediated energy pathways on community dynamics and energy transfer to higher trophic levels is of high importance considering eutrophication and global warming induced shifts to dominance of unfavourable prey such as cyanobacteria. We theoretically investigated community dynamics and energy transfer in a food web consisting of an edible-nonhost and an inedible-host phytoplankton species, a fungal parasite, and a zooplankton species grazing on edible phytoplankton and fungi. Food web dynamics were investigated along a nutrient gradient for two cases: (1) non-adaptive zooplankton species representative for filter feeders like cladocerans and (2) zooplankton with the ability to actively adapt their feeding preferences like many copepod species. For both feeding strategies, the importance of the mycoloop for zooplankton increases with nutrient availability. This increase is smooth for non-adaptive consumers. For a consumer with an adaptive feeding preference, we observe an abrupt shift from almost exclusive preference for edible phytoplankton (dominant prey) at low nutrient levels to a strong preference for parasitic fungi at high nutrient levels. The model predicts that parasitic fungi can contribute up to 50% of the zooplankton diet in nutrient rich environments, agreeing with empirical observations on zooplankton gut content from eutrophic systems during cyanobacterial blooms. Our findings highlight the role of parasite-mediated energy pathway for predictions on energy flow and community composition under environmental change.

Speciation is a fundamental evolutionary process, which results in genetic differentiation of populations and manifests as discrete morphological, physiological and behavioral differences. Each species has had its own evolutionary trajectory, formed by many types of selection pressures and random drift, making the association of genetic differences between the species with the phenotypic differences extremely difficult. In the present study, we have used an in vitro model to analyze in depth the genetic and gene regulation differences between fibroblasts of two closely related mammals, the arctic/subarctic mountain hare (Lepus timidus Linnaeus) and the temperate steppe-climate adapted brown hare (Lepus europaeus Pallas). We discovered the existence of a species-specific expression pattern of 1,623 genes, manifesting in differences in cell growth, respiration, and metabolism. Interspecific differences in the housekeeping functions of fibroblast cells suggest speciation acts on fundamental processes, even in these two interfertile species. Our results help to understand the molecular constituents of a species difference on cellular level, which could contribute to the maintenance of the species boundary

When major emergencies or accidents occur, risk evaluation and prediction are the most important means to reduce the impact of these disasters. Typical risk evaluation uses the failure mode and effects analysis (FMEA) method for failure risk ranking and control. However, when faced with severe special infectious diseases such as COVID-19, there will be many cognitive and information uncertainties that the FMEA method is unable to effectively handle. To effectively deal with the issue of risk evaluation during the COVID‐19 pandemic, this paper integrated the risk priority number and spherical fuzzy sets methods to propose a novel emergency risk evaluation method. In the numerical verification, this paper applied the example of avoiding secondary COVID-19 transmissions in the hospital to explain the calculation procedure and validity of the proposed new emergency risk evaluation approach. The calculation results were also compared with the typical RPN, fuzzy set, and intuitionistic fuzzy set methods. The calculation results showed that the proposed new emergency risk evaluation approach could effectively handle the cognitive and information uncertainties of emergency risk evaluation issues during the COVID-19 pandemic.

The vagina links the organs where gynecologic tumors are located to the outside world. A healthy acidic vaginal environment relies on lactobacilli; a dysregulated vaginal flora is associated with the occurrence, unsatisfactory treatment and poor prognosis of gynecologic malignancies. Using microbial markers to screen the difficult-to-detect characteristics of early tumors may play a key role in prolonging the survival of cancer patients. The discovery of microbes within tumor has led to the consideration of the immunological relevance of internal microorganisms to tumors. This article aims to review the relevance of microorganisms within the above two environments to gynecologic malignancies.