bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning approaches identify male body size as the most accurate predictor of species richness
Authors: Čandek Klemen , Pristovšek Čandek Urška , Kuntner Matjaž 
Published: August 2020

Abstract
Background
A major challenge in biodiversity science is to understand the factors contributing to the variability of species richness –the number of different species in a community or region - among comparable taxonomic lineages. Multiple biotic and abiotic factors have been hypothesized to have an effect on species richness and have been used as its predictors, but identifying accurate predictors is not straightforward. Spiders are a highly diverse group, with some 48,000 species in 120 families; yet nearly 75% of all species are found within just the ten most speciose families. Here we use a Random Forest machine learning algorithm to test the predictive power of different variables hypothesized to affect species richness of spider genera.

Results
We test the predictive power of 22 variables from spiders’ morphological, genetic, geographic, ecological and behavioral landscapes on species richness of 45 genera selected to represent the phylogenetic and biological breath of Araneae. Among the variables, Random Forest analyses find body size (specifically, minimum male body size) to best predict species richness. Multiple Correspondence analysis confirms this outcome through a negative relationship between male body size and species richness. Multiple Correspondence analyses furthermore establish that geographic distribution of congeneric species is positively associated with genus diversity, and that genera from phylogenetically older lineages are species poorer. Of the spider-specific traits, neither the presence of ballooning behavior, nor sexual size dimorphism, can predict species richness.

Conclusions
We show that machine learning analyses can be used in deciphering the factors associated with diversity patterns. Since no spider-specific biology could predict species richness, but the biologically universal body size did, we believe these conclusions are worthy of broader biological testing. Future work on other groups of organisms will establish whether the detected associations of species richness with small body size and wide geographic ranges hold more broadly.
Assessment of a biofluid mechanics-based model for calculating portal pressure in canines
Authors: Lin Jia-Yun , Zhang Chi-Hao , Zheng Lei , Song Chen-Lu , Deng Wen-Sheng , Zhu Yi-Ming , Zheng Li , Wu Li-Zhong , Sun Long-Ci , Luo Meng 
Published: August 2020

Abstract
Background
Portal hypertension is a severe complication caused by various chronic liver diseases. The standard methods for detecting portal hypertension (hepatic venous pressure gradient and free portal pressure) are available in only a few hospitals due to their technical difficulty and invasiveness; thus, non-invasive measuring methods are needed. This study aimed to establish and assess a novel model to calculate free portal pressure based on biofluid mechanics.

Result
Comparison of each dog’s virtual and actual free portal pressure showed that a biofluid mechanics-based model could accurately predict free portal pressure (mean difference: -0.220, 95% CI: − 0.738 to 0.298; upper limit of agreement: 2.24, 95% CI: 1.34 to 3.14; lower limit of agreement: -2.68, 95% CI: − 3.58 to − 1.78; intraclass correlation coefficient: 0.98, 95% CI: 0.96 to 0.99; concordance correlation coefficient: 0.97, 95% CI: 0.93 to 0.99) and had a high AUC (0.984, 95% CI: 0.834 to 1.000), sensitivity (92.3, 95% CI: 64.0 to 99.8), specificity (91.7, 95% CI: 61.5 to 99.8), positive likelihood ratio (11.1, 95% CI: 1.7 to 72.8), and low negative likelihood ratio (0.08, 95% CI: 0.01 to 0.6) for detecting portal hypertension.

Conclusions
Our study suggests that the biofluid mechanics-based model was able to accurately predict free portal pressure and detect portal hypertension in canines. With further research and validation, this model might be applicable for calculating human portal pressure, detecting portal hypertensive patients, and evaluating disease progression and treatment efficacy.
Surgical castration versus chemical castration in donkeys: response of stress, lipid profile and redox potential biomarkers
Authors: Abou-Khalil Nasser S. , Ali Marwa F. , Ali Magda M. , Ibrahim Ahmed 
Published: August 2020

Abstract
Background
Castration is a husbandry practice raising important questions on the welfare and physiological status of farm animals. Searching for effective castration methods that minimally compromise the body physiology is worthy of attention. Therefore, this study aimed to evaluate the differential response of biological systems in donkeys to surgical castration versus the chemical one by CaCl2 with special emphasis on stress, lipid profile, and oxidative stress biomarkers. Donkeys were divided randomly and equally into two groups; the chemical (Ch) and surgical (S) groups (n = 6). The Ch group was chemically castrated by intratesticular injection of 20% CaCl2 dissolved in absolute ethanol. Blood samples were collected prior to castration and at 15, 30, 45, and 60 days after the beginning of experiment.

Results
Surprisingly, the Ch group at the end of the experiment was characterized by significantly higher cortisol level compared to the S group. TC and LDL-C levels in the S group significantly decreased at day 45, while TG levels significantly increased at days 45 and 60 in comparison with day 0. HDL-C levels at days 30 and 60 in the Ch group significantly increased in comparison with day 0. At day 30 post-castration, HDL-C was significantly higher and LDL-C was significantly lower in the Ch group than the S group. A significant elevation in TC and LDL-C was observed at day 45 and in HDL-C at the end of experimental duration in the Ch group when compared with the S group. TPX level was significantly lower and TAC was significantly higher in the Ch group at day 45 than the S group.

Conclusion
Surgical castration evoked less stress and minor changes in lipid profile and oxidant/antioxidant balance relative to chemical castration by intratesticular 20% CaCl2 dissolved in absolute ethanol.
A novel neoantigen discovery approach based on chromatin high order conformation
Authors: Shi Yi , Zhang Mingxuan , Meng Luming , Su Xianbin , Shang Xueying , Guo Zehua , Li Qingjiao , Lin Mengna , Zou Xin , Luo Qing , Yu Yaoliang , Wu Yanting , Da Lintai , Cai Tom Weidong , He Guang , Han Ze-Guang 
Published: August 2020

AbstractBackgroundHigh-throughput sequencing technology has yielded reliable and ultra-fast sequencing for DNA and RNA. For tumor cells of cancer patients, when combining the results of DNA and RNA sequencing, one can identify potential neoantigens that stimulate the immune response of the T cell. However, when the somatic mutations are abundant, it is computationally challenging to efficiently prioritize the identified neoantigen candidates according to their ability of activating the T cell immuno-response.MethodsNumerous prioritization or prediction approaches have been proposed to address this issue but none of them considers the original DNA loci of the neoantigens from the perspective of 3D genome. Based on our previous discoveries, we propose to investigate the distribution of neoantigens with different immunogenicity abilities in 3D genome and propose to adopt this important information into neoantigen prediction.ResultsWe retrospect the DNA origins of the immuno-positive and immuno-negative neoantigens in the context of 3D genome and discovered that DNA loci of the immuno-positive neoantigens and immuno-negative neoantigens have very different distribution pattern. Specifically, comparing to the background 3D genome, DNA loci of the immuno-positive neoantigens tend to locate at specific regions in the 3D genome. We thus used this information into neoantigen prediction and demonstrated the effectiveness of this approach.ConclusionWe believe that the 3D genome information will help to increase the precision of neoantigen prioritization and discovery and eventually benefit precision and personalized medicine in cancer immunotherapy.
Active case detection of malaria in pregnancy using loop-mediated amplification (LAMP): a pilot outcomes study in South West Ethiopia
Authors: Tadesse Guluma , Kamaliddin Claire , Doolan Cody , Amarasekara Ranmalee , Legese Ruth , Mohon Abu Naser , Cheaveau James , Yewhalaw Delenasaw , Pillai Dylan R. 
Published: August 2020

Abstract
Background
125 million women are pregnant each year in malaria endemic areas and are, therefore, at risk of Malaria in Pregnancy (MiP). MiP is the direct consequence of Plasmodium infection during pregnancy. The sequestration of Plasmodium falciparum parasites in the placenta adversely affects fetal development and impacts newborn birth weight. Importantly, women presenting with MiP commonly develop anaemia. In Ethiopia, the Ministry of Health recommends screening symptomatic women only at antenatal care visits with no formal intermittent preventive therapy. Since MiP can display low-level parasitaemia, current tests which include microscopy and RDT are challenged to detect these cases. Loop mediated isothermal Amplification (LAMP) technology is a highly sensitive technique for DNA detection and is field compatible. This study aims to evaluate the impact of active malaria case detection during pregnancy using LAMP technology in terms of birth outcomes.

Methods
A longitudinal study was conducted in two health centres of the Kafa zone, South West Ethiopia. Both symptomatic and asymptomatic pregnant women were enrolled in the first or second trimester and allocated to either Standard of Care (SOC—microscopy and RDT) or LAMP (LAMP, microscopy and RDT). Women completed at least three visits prior to delivery, and the patient was referred for treatment if Plasmodium infection was detected by any of the testing methods. The primary outcome was to measure absolute birth weight, proportion of low birth weight, and maternal/neonatal haemoglobin in each arm. Secondary outcomes were to assess the performance of microscopy and RDT versus LAMP conducted in the field.

Results
One hundred and ninety-nine women were included and assigned to either LAMP or SOC. Six were lost to follow up. In this cohort, 66.8% of women did not display any clinical symptoms and 70.9% were multi-parous. A reduced proportion of low birth weight newborns was observed in the LAMP group (0%) compared to standard of care (14%) (p <0.001). Improved neonatal haemoglobin was observed in the LAMP (13.1 g/dL) versus the SOC (12.8 g/dL) (p = 0.024) arm. RDT and microscopy had an analytical sensitivity of 66.7% and 55.6% compared to LAMP as a reference standard.

Conclusions
These results support the use of highly sensitive tools for rapid on-site active case detection of MiP which may improve birth outcomes in the absence of IPT. However, further large-scale studies are required to confirm this finding.
Evaluating the predictive performance of malaria antibodies and FCGR3B gene polymorphisms on Plasmodium falciparum infection outcome: a prospective cohort study
Authors: Dwomoh Duah , Adu Bright , Dodoo Daniel , Theisen Michael , Iddi Samuel , Gerds Thomas A. 
Published: August 2020

AbstractBackgroundMalaria antigen-specific antibodies and polymorphisms in host receptors involved in antibody functionality have been associated with different outcomes ofPlasmodium falciparuminfections. Thus, to identify key prospective malaria antigens for vaccine development, there is the need to evaluate the associations between malaria antibodies and antibody dependent host factors with more rigorous statistical methods. In this study, different statistical models were used to evaluate the predictive performance of malaria-specific antibodies and host gene polymorphisms onP. falciparuminfection in a longitudinal cohort study involving Ghanaian children.MethodsModels with different functional forms were built using known predictors (age, sickle cell status, blood group status, parasite density, and mosquito bed net use) and malaria antigen-specific immunoglobulin (Ig) G and IgG subclasses andFCGR3Bpolymorphisms shown to mediate antibody-dependent cellular functions. Malaria antigens studied were Merozoite surface proteins (MSP-1 and MSP-3), Glutamate Rich Protein (GLURP)-R0, R2, and the Apical Membrane Antigen (AMA-1). The models were evaluated through visualization and assessment of differences between the Area Under the Receiver Operating Characteristic Curve and Brier Score estimated by suitable internal cross-validation designs.ResultsThis study found that theFCGR3B-c.233C>A genotype and IgG against AMA1 were relatively better compared to the other antibodies andFCGR3Bgenotypes studied in classifying or predicting malaria risk among children.ConclusionsThe data supports theP. falciparum, AMA1 as an important malaria vaccine antigen, whileFCGR3B-c.233C>A under the additive and dominant models of inheritance could be an important modifier of the effect of malaria protective antibodies.
A comprehensive assessment of predictors of fertility outcomes in men with non-obstructive azoospermia undergoing microdissection testicular sperm extraction
Authors: Kavoussi Parviz K. , West Brady T. , Chen Shu-Hung , Hunn Caitlin , Gilkey Melissa S. , Machen G. Luke , Kavoussi Keikhosrow M. , Esqueda Amy , Wininger J. David , Kavoussi Shahryar K. 
Published: August 2020

AbstractBackgroundMicrodissection testicular sperm extraction (microTESE) in men with non-obstructive azoospermia (NOA) is the procedure that results in the highest number of sperm cells retrieved for in vitro fertilization (IVF). This study presents a novel assessment of predictors of sperm retrieval as well as downstream embryology and pregnancy outcomes in cases of men with NOA undergoing microTESE.MethodsA retrospective chart review of 72 men who underwent microTESE for predictors of fertility outcomes including sperm retrieved at microTESE, embryology progression to embryo transfer (ET), clinical pregnancy, live birth, and surplus sperm retrieved for additional IVF/intracytoplasmic injection cycles beyond one initial cycle. Statistical models for each of these outcomes were fitted, with ap-value of < 0.05 considered significant for the parameters estimated in each model.ResultsSeventy-two men underwent microTESE, and 51/72 (70.8%) had sperm retrieved. Of those, 29/43 (67.4%) reached ET. Of the couples who underwent ET, 21/29 (72.4%) achieved pregnancy and 18/29 (62.1%) resulted in live birth. Of the men with sperm retrieved, 38/51 (74.5%) had surplus sperm cryopreserved beyond the initial IVF cycle.Age, testicular volume, FSH, and testicular histopathology were assessed as predictors for sperm retrieved at microTESE, progression to ET, pregnancy, live birth, and surplus sperm. There were no preoperative predictors of sperm retrieval, clinical pregnancy, or live birth. Age predicted reaching ET, with older men having increased odds. FSH level had a negative relationship with surplus sperm retrieved. Men with hypospermatogenesis histology had higher rates of sperm retrieval, clinical pregnancy, live birth, and having surplus sperm.ConclusionsMen who underwent microTESE with a hypospermatogenesis histopathology had better outcomes, including higher rates of sperm retrieval, clinical pregnancy, live birth, and having surplus sperm retrieved. Increasing male partner age increased the odds of reaching ET. No other clinical factors were predictive for the outcomes considered.
Health technology assessment of biosimilars worldwide: a scoping review
Authors: Ascef Bruna de Oliveira , Lopes Ana Carolina de Freitas , de Soárez Patrícia Coelho 
Published: August 2020

Abstract
Background
Health technology assessment (HTA) should provide an assessment of a technology’s effects on health and of the related social, economic, organisational and ethical issues. HTA reports on biosimilars can specifically assess their immunogenicity, their extrapolation to one or more conditions, and the risks of interchangeability and substitution. We aimed to complete a scoping review within the context of HTA organisations to synthesise HTA reports on biosimilars and to map the extension, scope and methodological practices.

Main body
A scoping review methodology was applied. The sources for biosimilars HTA reports were database searches and grey literature from HTA organisation websites up to June 2019. HTA reports of biosimilars were classified as full HTA, mini-HTA or rapid reviews. Data were extracted and recorded on a calibrated predefined data form. We identified 70 HTA reports of biosimilars of 16 biologic products (65.71% in 2015–2018) produced by 13 HTA organisations from 10 countries; 2 full HTAs, 4 mini-HTAs and 64 rapid reviews met the inclusion criteria. Almost all the rapid reviews gave no information regarding any evidence synthesis method and approximately half of the rapid reviews did not appraise the risk of bias of primary studies or the overall quality of evidence. All full-HTAs and mini-HTAs addressed organisational, ethical, social and legal considerations, while these factors were assessed in less than half of the rapid reviews. The immunogenicity and extrapolation of one or more conditions were often considered. The majority of full-HTAs and mini-HTAs contained an assessment of switching and a discussion of an educational approach about biosimilars. No HTA report rejected the adoption/reimbursement of the biosimilar assessed.

Conclusion
HTA of biosimilars are emerging in the context of HTA organisations and those that exist often duplicate reports of the same biosimilar. Most HTA reports of biosimilars do not conduct a systematic literature review or consider economic issues. No report has rejected the adoption/reimbursement of biosimilars. There is a need to standardise the minimum criteria for the development of HTA on biosimilars to ensure a better understanding and better decision-making.
Psychosocial barriers and enablers of exclusive breastfeeding: lived experiences of mothers in low-income townships, North West Province, South Africa
Authors: Witten Chantell , Claasen Nicole , Kruger Herculina S. , Coutsoudis Anna , Grobler Herman 
Published: August 2020

AbstractBackgroundDespite national efforts to promote exclusive breastfeeding (EBF), South Africa’s EBF rate is only 32 %. The aim of this study was to examine the rate of EBF discontinuation and the lived experiences of breastfeeding mothers at postnatal time points 3–14 days, 4–8 weeks, 10–14 weeks and 20–24 weeks.MethodsThis community-based mixed-methods study collected data within a prospective cohort study on sociodemographics, the Edinburgh Postnatal Depression Scale (EPDS) and the Breastfeeding Self-Efficacy Scale-Short Form (BSES-SF) at 6–8 weeks with infant feeding data collected at 4–8, 10–14 and 20–24 weeks from 159 mothers living in low income areas. Six focus groups with 32 mothers with infants aged 6–24 weeks were conducted. Descriptive statistics was used for the quantitative data and thematic analysis for qualitative data.ResultsThe majority of mothers were unmarried (84.9%), living with family (69.2%) and unemployed (74.2%). Exclusive breastfeeding decreased from 34% at 4–8 weeks to 9.7% at 20–24 weeks. Mixed feeding with infant formula increased from 17.0 to 30.6% and food feeding from 3.1 to 54.2%. While there were no statistically significant associations between EBF and any of the quantitative sociodemographic variables, in the qualitative data, codes associated with barriers were more than enablers. The themes wereMothers’ attributes (wellbeing, experiences and relationships)with the codemother’s stressthe strongest barrier,Mother’s knowledge, attitudes and practices of breastfeedingwith the codeconventional medicinesthe strongest barrier,Family environmentwith the codehome settingthe strongest barrier,Social environmentwithpublic spaces and placesa barrier and inBaby cuesthe codebaby stomach ailmentsthe barrier. Within these same themesmother’s positive emotions,benefits of breastfeeding,support in the home, access to information and services fromhealth professionalsandbaby’s healthwere strong enabling factors.ConclusionsLow EBF, high mixed feeding and a high EPDS score were explained by the barriers identified in the qualitative data. The data suggests that mothers from low-income households would be better supported through interventions that address food insecurity; family relationships and those that build confidence in mothers and resilience in confronting difficult and hostile breastfeeding environments.
Haematoma block: a safe method for pre-surgical reduction of distal radius fractures
Authors: Maleitzke Tazio , Plachel Fabian , Fleckenstein Florian Nima , Wichlas Florian , Tsitsilonis Serafeim 
Published: August 2020

Abstract
Background
The haematoma block (HB) has been successfully used to minimise pain prior to otherwise painful closed reduction manoeuvres for distal radius fractures. However, the invasive manner of the procedure, which technically produces an open fracture, still raises the question, whether HBs increase the risk of infection compared to conventional intravenous analgesia (IA). The purpose of this study was to assess complication rates and safety of the HB procedure for the closed reduction of surgically treated distal radius fractures.

Methods
We included 176 distal radius fractures in 170 patients in a retrospective mono-centric study, who underwent closed reduction and casting followed by definitive surgical care over a period of two years. Patients either received a HB or IA before closed reduction and were evaluated for minor and major complications over a follow-up period of four years.

Results
Overall, 42 distal radius fractures were treated with a HB (23.9%) and 134 with IA (76.1%) before closed reduction. There were a single major (2.3%) and eight minor (19%) complications observed in the HB group compared to two major (1.4%) and 24 minor (17.9%) complications in the IA group. No significant differences were identified between the two groups. Sex and type of fracture had no effect on complication rates, however, younger patients experienced higher complication rates in comparison to older ones (p = 0.035).

Conclusion
According to our data, the apprehensions that clinicians may have of creating open fractures through HB procedures, are unnecessary and may be abandoned confidently.