bluuebunny/crossref_metadata_2025_split huggingface dataset:
The true incidence of recurrent implantation failure
Authors: Macklon Nick S. 
Published: May 2022

Purpose of review
To review the merits and limitations of current definitions of recurrent implantation failure (RIF), how they translate into estimates of incidence and to summarize how emerging concepts of individualizing the recognition of this condition can assist in changing the way RIF is identified, studied and managed.

Recent findings
The notion of a one size fits all definition of RIF is seen to be of limited clinical value, as the individual risk of repeated IVF failure has many determinants and causes. Novel approaches provide a means of identifying ‘actionable’ RIF in individual patients.

Summary
Uncertainties as to what constitutes, causes and defines RIF have served to limit progress in its management. A new approach promises to permit progress from the current impasse.
Evaluation of endometrial receptivity and implantation failure
Authors: Bui Anthony H. , Timmons Douglas B. , Young Steven L. 
Published: May 2022

Purpose of review
To succinctly review the basic mechanisms of implantation and luteal phase endometrial differentiation, the etiologies of impaired endometrial function and receptivity, and the current methods that exist to evaluate and treat impaired endometrial receptivity.

Recent findings
Human embryo implantation requires bidirectional communication between blastocyst and a receptive endometrium. Etiologies of impaired endometrial receptivity are varied. Some of these include delayed endometrial maturation, structural abnormalities, inflammation, and progesterone resistance. Current methods to evaluate endometrial receptivity include ultrasonography, hysteroscopy, and endometrial biopsy. Treatments are limited, but include operative hysteroscopy, treatment of endometriosis, and personalized timing of embryo transfer.

Summary
Although some mechanisms of impaired endometrial receptivity are well understood, treatment options remain limited. Future efforts should be directed towards developing interventions targeted towards the known mediators of impaired endometrial receptivity.
Neurological disorders and small bowel dysmotility
Authors: Kamperidis Nikolaos , Nightingale Jeremy 
Published: May 2022

Purpose of review
Small bowel dysmotility is common in the context of neurological disorders. Overlooking it can have an adverse impact on patient's quality of life and neurological outcomes. This review focuses on describing the mechanisms and effects of enteric dysmotility in neurological patients and providing treatment options.

Recent findings
Small bowel dysmotility is prevalent among neurological patients. The definition and diagnosis of small bowel dysmotility is a challenge; however, up to two-thirds of neurological patients may experience associated symptoms. Small bowel dysmotility can affect the absorption of nutrients and medication, impacts on social and professional function and can result in malnutrition and its associated morbidity and mortality.

Summary
Small bowel dysmotility due to a neuropathy can result from acute or chronic disorders in the central and peripheral nervous system and includes the cerebral cortex, brain stem, spinal cord, parasympathetic (vagus) and sympathetic nerves and the myenteric and submucosal plexuses of the intestine. Generalized muscle disorders can also cause an enteral myopathy. Generally, the disorders may be degenerative or inflammatory. Both enteric neuropathy and myopathy may cause symptoms of abdominal pain, nausea/vomiting, bloating, constipation or diarrhoea and can cause malnutrition. The symptoms need to be addressed in order of importance to the patient and malnutrition prevented or treated.
A training and implementation model for head and neck oncology service delivery in Mozambique
Authors: Chulam Thiago C. , Bambo Arquimedes Wamarremula Pedro , Machava Pedro Rafael , Kowalski Luiz P. 
Published: May 2022

Purpose of review
There is an extreme shortage of head and neck surgeons in Africa. In Mozambique prior to 2000, there were no surgeons with specific training in head and neck surgical oncology. Here, we introduce a training model and report our experience with implementation following the training of the first two head and neck surgeons from Mozambique.

Recent findings
This training program, undertaken in Brazil, facilitated the formation of the first two head and neck surgeons from Mozambique. These surgeons received comprehensive training in head and neck surgical oncology and multidisciplinary care, allowing them to then treat their patients under continuous online mentorship collaboration. This model is expected to help in the local formation of new specialists and in the establishment of this specialty in Mozambique.

Summary
The program started with remote training and support provided by the MD Anderson Cancer Center, in Texas, USA, as part of the Extension for Community Healthcare Outcomes program. Further training was then undertaken at an established fellowship program in Brazil as a focal point for 2 years, and the knowledge gained was replicated and disseminated locally.
Pediatric platelet transfusions in critical illness: a narrative review of recent studies
Authors: Atchison Christie , Mahmood Hera , Nellis Marianne E. 
Published: May 2022

Purpose of review
We sought to describe the current use of platelet transfusions, harms associated with platelet transfusion, new methods of platelet processing that attempt to address these harms, and recent platelet transfusion guidance specific to critically ill children.

Recent findings
Platelet transfusions have been associated with significant morbidity and mortality. New processing techniques, such as pathogen reduction, have been developed to combat infectious risks but in a recent trial of platelet transfusion thresholds in neonates, transfusing platelets more liberally was associated with increased bleeding and mortality.

Summary
Recent efforts to develop evidence-based guidelines for platelet transfusion in critically ill children were limited by the lack of evidence. However, given the significant risks, restrictive transfusion thresholds should be considered.
Bivalirudin in pediatric extracorporeal membrane oxygenation
Authors: Ryerson Lindsay M. , McMichael Ali B.V. 
Published: May 2022

Purpose of review
This review summarizes the current literature surrounding the use of bivalirudin as an alternative anticoagulant for pediatric extracorporeal membrane oxygenation (ECMO) patients.

Recent findings
Recent single center studies describe that bivalirudin may be associated with decreased blood product transfusion, decreased cost and similar clinical outcomes for pediatric ECMO patients who have failed unfractionated heparin (UFH) anticoagulation. aPTT is the most common test to monitor bivalirudin but has several limitations. Other tests including dilute thrombin time (dTT) and viscoelastic assays are promising but more study is needed. Current evidence suggests that bivalirudin is a well tolerated and effective alternative anticoagulant for pediatric ECMO patients who have failed UFH anticoagulation but prospective studies are needed to confirm these results.

Summary
Bivalirudin is a promising alternative anticoagulant for pediatric ECMO patients who have failed UFH. Large prospective, multicenter studies are needed to confirm safety and efficacy.
Genetic basis of speciation and adaptation: from loci to causative mutations
Authors: Kitano Jun , Ishikawa Asano , Ravinet Mark , Courtier-Orgogozo Virginie 
Published: May 2022

Does evolution proceed in small steps or large leaps? How repeatable is evolution? How constrained is the evolutionary process? Answering these long-standing questions in evolutionary biology is indispensable for both understanding how extant biodiversity has evolved and predicting how organisms and ecosystems will respond to changing environments in the future. Understanding the genetic basis of phenotypic diversification and speciation in natural populations is key to properly answering these questions. The leap forward in genome sequencing technologies has made it increasingly easier to not only investigate the genetic architecture but also identify the variant sites underlying adaptation and speciation in natural populations. Furthermore, recent advances in genome editing technologies are making it possible to investigate the functions of each candidate gene in organisms from natural populations. In this article, we discuss how these recent technological advances enable the analysis of causative genes and mutations and how such analysis can help answer long-standing evolutionary biology questions.This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.
The selfing syndrome and beyond: diverse evolutionary consequences of mating system transitions in plants
Authors: Tsuchimatsu Takashi , Fujii Sota 
Published: May 2022

The shift from outcrossing to self-fertilization (selfing) is considered one of the most prevalent evolutionary transitions in flowering plants. Selfing species tend to share similar reproductive traits in morphology and function, and such a set of traits is called the ‘selfing syndrome’. Although the genetic basis of the selfing syndrome has been of great interest to evolutionary biologists, knowledge of the causative genes or mutations was limited until recently. Thanks to advances in population genomic methodologies combined with high-throughput sequencing technologies, several studies have successfully unravelled the molecular and genetic basis for evolution of the selfing syndrome inCapsella,Arabidopsis,Solanumand other genera. Here we first introduce recent research examples that have explored the loci, genes and mutations responsible for the selfing syndrome traits, such as reductions in petal size or in pollen production, that are mainly relevant to pre-pollination processes. Second, we review the relationship between the evolution of selfing and interspecific pollen transfer, highlighting the findings of post-pollination reproductive barriers at the molecular level. We then discuss the emerging view of patterns in evolution of the selfing syndrome, such as the pervasive involvement of loss-of-function mutations and the relative importance of selection versus neutral degradation.This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.
Extensive simulations assess the performance of genome-wide association mapping in variousSaccharomyces cerevisiaesubpopulations
Authors: Peter Jackson , Friedrich Anne , Liti Gianni , Schacherer Joseph 
Published: May 2022

With the advent of high throughput sequencing technologies, genome-wide association studies (GWAS) have become a powerful paradigm for dissecting the genetic origins of the observed phenotypic variation. We recently completely sequenced the genome of 1011Saccharomyces cerevisiaeisolates, laying a strong foundation for GWAS. To assess the feasibility and the limits of this approach, we performed extensive simulations using five selected subpopulations as well as the total set of 1011 genomes. We measured the ability to detect the causal genetic variants involved in Mendelian and more complex traits using a linear mixed model approach. The results showed that population structure is well accounted for and is not the main problem when the sample size is high enough. While the genetic determinant of a Mendelian trait is easily mapped in all studied subpopulations, discrepancies are seen between datasets when performing GWAS on a complex trait in terms of detection, false positive and false negative rate. Finally, we performed GWAS on the different defined subpopulations using a real quantitative trait (resistance to copper sulfate) and showed the feasibility of this approach. The performance of each dataset depends simultaneously on several factors such as sample size, relatedness and population evolutionary history.This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.
Speciation and adaptation research meets genome editing
Authors: Ansai Satoshi , Kitano Jun 
Published: May 2022

Understanding the genetic basis of reproductive isolation and adaptive traits in natural populations is one of the fundamental goals in evolutionary biology. Genome editing technologies based on CRISPR-Cas systems and site-specific recombinases have enabled us to modify a targeted genomic region as desired and thus to conduct functional analyses of target loci, genes and mutations even in non-conventional model organisms. Here, we review the technical properties of genome editing techniques by classifying them into the following applications: targeted gene knock-out for investigating causative gene functions, targeted gene knock-in of marker genes for visualizing expression patterns and protein functions, precise gene replacement for identifying causative alleles and mutations, and targeted chromosomal rearrangement for investigating the functional roles of chromosomal structural variations. We describe examples of their application to demonstrate functional analysis of naturally occurring genetic variations and discuss how these technologies can be applied to speciation and adaptation research.This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.
Clinical and microbiological investigation into mixed growth urine cultures
Authors: Folaranmi Tolulope , Harley Clare , Jolly Jim , Kirby Andrew 
Published: May 2022

Introduction. Urine samples submitted for investigation of urinary tract infection (UTI) may identify more than one bacterial isolate. These samples may be reported as ‘mixed growth urine culture’ (MGUC). The clinical significance of MGUC remains controversial.

Hypothesis/Gap Statement. The impact of MGUC on patient management is not known and should be assessed.
To describe MGUC and assess its impact on patient management.

Methodology. Microbiology laboratory reports (Leeds, UK) were retrospectively analysed and urine cultures reported as MGUC from a 1 week period underwent detailed laboratory analysis. Semi-structured interviews of NHS clinicians’ response to MGUC reports were explored for emergent themes.

Results. In 2018, 12.4 % (14,323/115,664) of urine specimens processed to detect bacterial pathogens were reported as MGUC. Among a total of 200 MGUC samples identified within 1 week in 2019, detailed laboratory analysis identified 459 bacterial isolates. Enterococcus species (30.1 %) and

Escherichia coli

(27.5 %) were the most frequently isolated and the most frequent organism combination (24 %). In total, 65.5 % cultures contained two organisms and 82.5 % of all MGUC contained at least one

Enterobacterales

. Interviews found clinicians believed MGUC reports represented detection of many commensal bacteria. Clinicians indicated they were more likely to diagnose and treat a UTI when provided with urine culture reports derived from detailed microbial analysis of MGUC, including identity and antibiotic sensitivity of organisms.

Conclusions. This study highlights the potential underuse of information derived from microbiological analysis of urine samples. Interpretive commentary on reports together with education for interpretation of enhanced reports should be explored further to improve outcomes in patients with UTI.
Differences in non-linearities determine retinal cell types
Authors: Trapani Francesco , Spampinato Giulia , Yger Pierre , Marre Olivier 
Published: May 2022

AbstractClassifying neurons in different types is still an open challenge. In the retina, recent works have taken advantage of the ability to record a large number of cells to classify ganglion cells into different types based on functional information. While the first attempts in this direction used the receptive field properties of each cell to classify them, more recent approaches have proposed to cluster ganglion cells directly based on their response to standard stimuli. These two approaches have not been compared directly. Here we recorded the responses of a large number of ganglion cells and compared two methods for classifying them into types, one based on the receptive field properties, and the other one using their responses to standard stimuli. We show that the stimulus-based approach allows separating more types than the receptive field-based method, leading to a better classification. This better granularity is due to the fact that the stimulus-based method takes into account not only the linear part of ganglion cell function, but also non-linearities. A careful characterization of non-linear processing is thus key to allow functional classification of sensory neurons.
Improving Interdisciplinary Teaching through a Complexity Lens
Authors: Neitzel Sarah , Zhao Yuhao , Eaton Carrie Diaz 
Published: May 2022

AbstractIn this article, we discuss the use of bipartite network analysis to understand and improve interdisciplinary teaching practice. We theorize mathematics and biology as part of a coevolving mutualistic ecosystem. As part of an interdisciplinary teaching initiative, we inventoried mathematics topics appearing in the marine biology classroom and their associated marine context. We then apply techniques of mutualistic bipartite networks analysis to this system to understand the use of mathematical concepts in a marine biology classroom. By analyzing the frequency and distribution of mathematics topics, we see that a variety of mathematical concepts are used across the course with most appearing only a few times. While this is an inherent trait of mutualistic coevolutionary networks, it can create a logistical challenge to supporting mathematics in the marine biology classroom. We find that marine biology topics containing the most mathematics are either close to the instructor’s research area or were introduced through externally developed educational resources. Finally, we analyze groups of topics that appear connected to each other more frequently to inform both interdisciplinary education development as well as disciplinary support. We also suggest ways to use network metrics to track interdisciplinary connections over time, helping us understand the impact of interventions on interdisciplinary teaching practice.
Ultraviolet Rate Constants of Pathogenic Bacteria: A Database of Genomic Modeling Predictions
Authors: Kowalski Wladyslaw , Bahnfleth William P. , Brais Normand , Walsh Thomas J. 
Published: May 2022

AbstractA database of bacterial ultraviolet (UV) susceptibilities is developed from an empirical model that correlates genomic parameters with UV rate constants. Software is used to count and evaluate potential ultraviolet photodimers and identifying hot spots in bacterial genomes. The method counts dimers that potentially form between adjacent bases that occur at specific genomic motifs such as TT, TC, CT, & CC. Hot spots are identified where clusters of three or more consecutive pyrimidines can enhance absorption of UV photons. The model incorporates nine genomic parameters into a single variable for each species that represents its relative dimerization potential. The bacteria model is based on a curve fit of the dimerization potential to the ultraviolet rate constant data for 92 bacteria species represented by 216 data sets from published studies. There were 4 outliers excluded from the model resulting in a 98% Confidence Interval. The curve fit resulted in a Pearson correlation coefficient of 80%. All identifiable bacteria important to human health, including zoonotic bacteria, were included in the database and predictions of ultraviolet rate constants were made based on their specific genomes. This database is provided to assist healthcare personnel and researchers in the event of outbreaks of bacteria for which the ultraviolet susceptibility is untested and where it may be hazardous to assess due to virulence. Rapid sequencing of the complete genome of any emerging pathogen will now allow its ultraviolet susceptibility to be estimated with equal rapidity. Researchers are invited to challenge these predictions.ImportanceThis research demonstrates the feasibility of using the complete genomes of bacteria to determine their susceptibility to ultraviolet light. Ultraviolet rate constants can now be estimated in advance of any laboratory test. The genomic methods developed herein allow for the assembly of a complete database of ultraviolet susceptibilities of pathogenic bacteria without resorting to laboratory tests. This UV rate constant information can be used to size effective ultraviolet disinfection systems for any specific bacterial pathogen when it becomes a problem.
Identification and Assessment of Systematic Measurement Error on Electrophysiological Recordings of Neural Cell Cultures
Authors: Stone Tyler , Kiehl Thomas R. , Bergeron Charles 
Published: May 2022

AbstractMicroelectrode arrays (MEA) hold great promise for a broad range of applications that require reliable characterization of the growth and function of neurons in culture. Widespread adoption of this platform depends on analytical methods to extract meaning from highly variable and noisy observations. In analyzing a comprehensive database of MEA recordings, we discovered that 22% of the electrodes presented systematic patterns of under- or non-detection of spike activity. Going undetected, principal components analysis (PCA) of these data reveal trends that would have lead to incorrect biological interpretations. We fully document thesedefectiveor biased electrodes, and distinguish two forms of defectiveness, via representations that aid in detecting them. We also showcase our approach for analyzing these data that permit for post-analytic review and correction. Repeating our PCA oncleaneddata, we discover a more complex interplay of biological variability. Finally, we make a case for transparency in data reporting and propose best practices for experimental and analysis phases.
Role for DNA double strand end-resection activity of RecBCD in control of aberrant chromosomal replication initiation in Escherichia coli
Authors: Goswami Sayantan , Gowrishankar Jayaraman 
Published: May 2022

AbstractReplication of the circular bacterial chromosome is initiated from a locus oriC with the aid of an essential protein DnaA. One approach to identify factors acting to prevent aberrant oriC-independent replication initiation in Escherichia coli has been that to obtain mutants which survive loss of DnaA. Here we show that a ΔrecD mutation, associated with attenuation of RecBCD’s DNA double strand end-resection activity, provokes abnormal replication and rescues ΔdnaA lethality in two situations: (i) in absence of 5’-3’ single-strand DNA exonuclease RecJ, or (ii) when multiple two-ended DNA double strand breaks (DSBs) are generated either by I-SceI endonucleolytic cleavages or by radiomimetic agents phleomycin or bleomycin. One-ended DSBs in the ΔrecD mutant did not rescue ΔdnaA lethality. With two-ended DSBs in the ΔrecD strain, ΔdnaA viability was retained even after linearization of the chromosome. Data from genome-wide DNA copy number determinations in ΔdnaA-rescued cells lead us to propose a model that nuclease-mediated DNA resection activity of RecBCD is critical for prevention of a σ-mode of rolling-circle over-replication when convergent replication forks merge and fuse, as may be expected to occur during normal replication at the chromosomal terminus region or during repair of two-ended DSBs following “ends-in” replication.