bluuebunny/crossref_metadata_2025_split huggingface dataset:
Palatoplasty Using Alveolar Ridge Incisions: A Novel Approach for Addressing Cleft Palate Deformities
Authors: Khetpal Sumun , Patel Harsh , DeLong Michael , Liu Mengyuan T. , Ozaki Wayne H. 
Published: April 2022

Background:
Traditionally, plastic surgeons have performed palatoplasties using mucoperiosteal flaps with lateral incisions that are medial to the alveolar ridge. However, narrow flaps can cause limitations in some cases. To construct larger and wider flaps and minimize exposed bone after closure, we propose a novel technique that entails creating the lateral incisions at the top of the alveolar ridge, instead of the base of the alveolar ridge, to capture more tissue when repairing the hard palate.

Methods:
A retrospective chart review was conducted for patients undergoing cleft palate repair with the aforementioned technique. Information collected included basic demographic and diagnostic factors related to cleft palate deformity and history of previous facial surgeries. Operative report details and postoperative complications were analyzed.

Results:
Nineteen patients with hard palate clefts were included in the analysis, with the majority being women (68%). There was a balanced representation of patients with Veau classifications of II (47%) and III (42%). The majority of patients had an isolated cleft palate (74%) and incomplete deformity (63%), with no other craniofacial deformities. One (5%) had postoperative self-limited oronasal fistula managed conservatively.

Conclusions:
We present a novel approach for repairing cleft palate deformities by extending the lateral incision to the top of the alveolar ridge to create larger mucosal flaps. Further longitudinal studies are needed to evaluate how this unique approach compares to traditional methods—with respect to impact on maxillary growth processes, requirement for subsequent surgeries beyond two years of follow-up, and ultimately normalized speech over time.
AMNIOTIC MEMBRANE GRAFT FOR THE TREATMENT OF LARGE REFRACTORY MACULAR HOLE
Authors: Khaqan Hussain Ahmad , Sahyoun Jean-Yves , Haider Muhammad Ali , Buksh Hasnain Muhammad 
Published: April 2022

PURPOSE:
Study off-label human amniotic membrane use outcomes for giant refractory macular hole closure.

Materials and Methods:
The study was performed at Lahore General Hospital, Lahore, over 52 months on patients who had undergone standard macular hole surgical procedures for treatment, but the hole failed to close. Refractory macular hole dimensions ranged from 824 µm to 1,568 µm. Before surgery, patients underwent slit-lamp examination, fundus photography, and optical coherence tomography for macular scan. Amniotic membrane graft (AMG) used in surgery was harvested from a human placenta 24 hours before. Before AMG application, enough internal limiting membrane peeling was performed to ensure perfect fitting and recovery. All holes were plugged with AMG and SF6 gas tamponade.

Results:
Twenty-nine patients, 20 men and nine women, were included in this study. Mean age of patients was 58 ± 6. Patients had refractory holes of average 1,237.48 ± 151.25 µm. Post-op, 100% macular hole closure was achieved in all patients. Type 1 closure was found in patients (37.93%) who underwent AMG surgery within 3 months after primary surgical failure. Type 2 closure was found in patients (62.07%) who were operated on 3 months after primary surgical failure.

Conclusion:
Refractory macular holes treated by AMG with SF6 gas tamponade achieve anatomical Type 1 closure if performed within 3 months of primary surgical repair.
Hypoxia and Polycythemia
Authors: Oren Shachar , Brenner Galit , Garty Yael , Scheier Eric 
Published: April 2022

Abstract
Point of care ultrasound (POCUS) can be useful in the differentiation between cardiac and pulmonary etiologies of hypoxia. Here, we present a child with signs of chronic hypoxia, found on POCUS to have multiple pulmonary arteriovenous malformations. A combination of POCUS and history supported a presumptive pediatric emergency department diagnosis of hereditary hemorrhagic telangiectasia. This case is the first case of a pulmonary arteriovenous malformation found on POCUS and reinforces the importance of POCUS as a first-line examination in the evaluation of chronic hypoxia in the pediatric emergency department.
Four-Quadrant Approach Squared: Ethical Analysis of Living Donation in Vascularized Composite Allotransplantation
Authors: Beederman Maureen , Teven Chad M. , Gottlieb Lawrence J. 
Published: April 2022

Summary:
Vascularized composite allotransplantation has become a widely accepted method for reconstruction or restoration of body parts, and the various ethical dilemmas that accompany vascularized composite allotransplantation have been widely discussed. As advancements in immunosuppression and tolerance continue to be made, the concept of living donor vascularized composite allotransplantation will likely become a popular option of the “reconstructive elevator.” In this article, the authors discuss the various ethical implications of living donor vascularized composite allotransplantation.
Assessment of Gender Disparities and Geographic Variations in Payments from Industry among Plastic Surgeons in the United States
Authors: Cunning Jessica R. , Rios-Diaz Arturo J. , Othman Sammy , Rappaport Gal , Gaughan John P. , Matthews Martha S. 
Published: April 2022

Background:
Various medical specialties have demonstrated gender disparities involving industry-supported payments. The authors sought to determine whether such disparities exist within plastic surgery.

Methods:
Industry contributions to plastic surgeons practicing in the United States were extracted from the Centers for Medicare and Medicaid Services Open Payments 2013 to 2017 databases. Specialists’ gender was obtained through online searches. Kruskal-Wallis tests compared payments (in U.S. dollars) by gender (overall and by payment category). Linear regression estimated the independent association of female gender with increased/reduced payments while controlling for state-level variations.

Results:
Of 1518 plastic surgeons, 13.4 percent were female. Of $44.4 million total payments from the industry, $3.35 million were made to female plastic surgeons (p < 0.01). During the study period, female plastic surgeons received lower overall payments than male plastic surgeons [median, $3500 (interquartile range, $800 to $9500) versus $4160.60 (interquartile range, $1000 to $19,728.20); p < 0.01]. This trend persisted nationwide after normalizing for year [$2562.50/year (interquartile range, $770 to $5916.25/year) versus $3200/year (interquartile range, $955 to $8715.15/year); p = 0.02] and at the state level in all 38 states where there was female representation. Analysis of payment categories revealed that honoraria payments were significantly higher for male plastic surgeons [$4738 (interquartile range, $1648 to $16,100) versus $1750 (interquartile range, $750 to $4100); p = 0.02]. Within risk-adjusted analysis, female plastic surgeons received $3473.21/year (95 percent CI, $671.61 to $6274.81; p = 0.02) less than male plastic surgeons.

Conclusions:
Gender disparities involving industry payments exist in plastic surgery at both national and state levels. Factors contributing to this phenomenon must be explored to understand implications of this gap.
Working Smarter, Not Harder: Using Data-Driven Strategies to Generate Front-End Cost Savings through Price Negotiation and Supply Chain Optimization
Authors: Reece Edward M. , Davis Matthew J. , Abu-Ghname Amjed , Castanon Joe M. , Voris Matthew , Hoxworth Ron , Winocour Sebastian , Buchanan Edward P. 
Published: April 2022

Background:
Supply chain optimization is an effective method of generating front-end cost savings and increasing hospital profits. Through the negotiation and renegotiation of supply chain contracts, plastic surgeons can dramatically change the price at which they purchase surgical supplies and implants. This study characterizes the potential impact of supply chain optimization and puts forth a generalizable, systematic approach for successful sourcing.

Methods:
From October of 2017 to September of 2018, the authors examined all patients taken to the operating room for either a facial fracture or a hand fracture. Cost data were collected, Supply Chain Information Management numbers were used to determine whether each item used during the study period was under contract, and cost savings based on contract negotiation were calculated. Potential cost savings were calculated using the BillOnly calculator.

Results:
For the 77 facial trauma cases and 63 hand trauma cases performed, a total of 330 items (70 distinct items) were used, 47 percent of which were under contract (47 percent contract use), with an average negotiated discount of 49 percent. Based on BillOnly material cost estimates, the authors’ institution would need to increase its contract use to 70 percent to achieve a net savings of 19 percent, and to 90 percent to achieve a net savings of 39 percent. The authors also estimated that if contract use increased to 90 percent, net savings would increase commensurately with increases in the average discount negotiated.

Conclusion:
Supply chain optimization offers plastic surgeons the potential to significantly decrease surgical costs while maintaining surgical quality.
The apportionment of citations: a scientometric analysis of Lewontin 1972
Authors: Carlson Jedidiah , Harris Kelley 
Published: April 2022

‘The apportionment of human diversity’ (1972) is the most highly cited research article published by geneticist Richard Lewontin in his career. This study's primary result—that most genetic diversity in humans can be accounted for by within-population differences, not between-population differences—along with Lewontin's outspoken, politically charged interpretations thereof, has become foundational to the scientific and cultural discourse pertaining to human genetic variation. The article has an unusual bibliometric trajectory in that it is much more salient in the bibliographic record today compared to the first 20 years after its publication. Here, we highlight four factors that may have played a role in shaping the paper's fame: (i) citations in influential publications across several disciplines; (ii) Lewontin's own popular books and media appearances; (iii) the renaissance of population genetics research of the early 1990s; and (iv) the serendipitous collision of scientific progress, influential books and papers, and heated controversies around the year 1994. We conclude with an analysis of Twitter data to characterize the communities and conversations that continue to keep this study at the centre of discussions about race and genetics, prompting new challenges for scientists who have inherited Lewontin's legacy.
This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
Covariance of pairwise differences on a multi-species coalescent tree and implications forFST
Authors: Guerra Geno , Nielsen Rasmus 
Published: April 2022

The multi-species coalescent (MSC) provides a theoretical foundation for modern phylogenetics and comparative population genetics. Its theoretical properties have been heavily studied but there are still aspects of the MSC that are largely unknown, including the covariances in pairwise coalescence times, which are fundamental for understanding the properties of statistics that combine data from multiple species, such as the fixation index (FST). The major contribution of this study is the derivation and implementation of exact expressions for the covariances of pairwise coalescence times under phylogenetic models with piecewise constant changes in population size, assuming no gene flow after species divergence. We use these expressions to derive the variance in average pairwise differences within and between populations. We then derive approximations for the expectation and bias of a sequence-based estimator ofFST, a commonly used genetic measurement of population differentiation, when it is applied to a non-recombining region of the genome. We show that the estimator ofFSTis generally biased downward. A freely available software package is provided, STCov, to calculate the mean, variances and covariances in coalescence times presented here under user-defined piecewise-constant species trees.This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
Population differentiation of polygenic score predictions under stabilizing selection
Authors: Yair Sivan , Coop Graham 
Published: April 2022

Given the many small-effect loci uncovered by genome-wide association studies (GWAS), polygenic scores have become central to genomic medicine, and have found application in diverse settings including evolutionary studies of adaptation. Despite their promise, polygenic scores have been found to suffer from limited portability across human populations. This at first seems in conflict with the observation that most common genetic variation is shared among populations. We investigate one potential cause of this discrepancy: stabilizing selection on complex traits. Counterintuitively, while stabilizing selection constrains phenotypic evolution, it accelerates the loss and fixation of alleles underlying trait variation within populations (GWAS loci). Thus even when populations share an optimum phenotype, stabilizing selection erodes the variance contributed by their shared GWAS loci, such that predictions from GWAS in one population explain less of the phenotypic variation in another. We develop theory to quantify how stabilizing selection is expected to reduce the prediction accuracy of polygenic scores in populations not represented in GWAS samples. In addition, we find that polygenic scores can substantially overstate average genetic differences of phenotypes among populations. We emphasize stabilizing selection around a common optimum as a useful null model to connect patterns of allele frequency and polygenic score differentiation.
This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
How methodological changes have influenced our understanding of population structure in threatened species: insights from tiger populations across India
Authors: Aylward Megan , Sagar Vinay , Natesh Meghana , Ramakrishnan Uma 
Published: April 2022

Unprecedented advances in sequencing technology in the past decade allow a better understanding of genetic variation and its partitioning in natural populations. Such inference is critical to conservation: to understand species biology and identify isolated populations. We review empirical population genetics studies of Endangered Bengal tigers within India, where 60–70% of wild tigers live. We assess how changes in marker type and sampling strategy have impacted inferences by reviewing past studies, and presenting three novel analyses including a single-nucleotide polymorphism (SNP) panel, genome-wide SNP markers, and a whole-mitochondrial genome network. At a broad spatial scale, less than 100 SNPs revealed the same patterns of population clustering as whole genomes (with the exception of one additional population sampled only in the SNP panel). Mitochondrial DNA indicates a strong structure between the northeast and other regions. Two studies with more populations sampled revealed further substructure within Central India. Overall, the comparison of studies with varied marker types and sample sets allows more rigorous inference of population structure. Yet sampling of some populations is limited across all studies, and these should be the focus of future sampling efforts. We discuss challenges in our understanding of population structure, and how to further address relevant questions in conservation genetics.
This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
The genetic legacy of the Manila galleon trade in Mexico
Authors: Rodríguez-Rodríguez Juan Esteban , Ioannidis Alexander G. , Medina-Muñoz Santiago G. , Barberena-Jonas Carmina , Blanco-Portillo Javier , Quinto-Cortés Consuelo D. , Moreno-Estrada Andrés 
Published: April 2022

The population of Mexico has a considerable genetic substructure due to both its pre-Columbian diversity and due to genetic admixture from post-Columbian trans-oceanic migrations. The latter primarily originated in Europe and Africa, but also, to a lesser extent, in Asia. We analyze previously understudied genetic connections between Asia and Mexico to infer the timing and source of this genetic ancestry in Mexico. We identify the predominant origin within Southeast Asia—specifically western Indonesian and non-Negrito Filipino sources—and we date its arrival in Mexico to approximately 13 generations ago (1620 CE). This points to a genetic legacy from the seventeenth century Manila galleon trade between the colonial Spanish Philippines and the Pacific port of Acapulco. Indeed, within Mexico we observe the highest level of this trans-Pacific ancestry in Acapulco, located in the state of Guerrero. This colonial Spanish trade route from East Asia to Europe was centred on Mexico and appears in historical records, but its legacy has been largely ignored. Identities and stories were suppressed due to slavery, assimilation of the immigrants as ‘Indios’ and incomplete historical records. Here we characterize this understudied Mexican ancestry.
This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
Polygenic risk, population structure and ongoing difficulties with race in human genetics
Authors: Kaplan Jonathan Michael , Fullerton Stephanie M. 
Published: April 2022

‘The Apportionment of Human Diversity’ stands as a noteworthy intervention, both for the field of human population genetics as well as in the annals of public communication of science. Despite the widespread uptake of Lewontin's conclusion that racial classification is of ‘virtually no genetic or taxonomic significance’, the biomedical research community continues to grapple with whether and how best to account for race in its work. Nowhere is this struggle more apparent than in the latest attempts to translate genetic associations with complex disease risk to clinical use in the form of polygenic risk scores, or PRS. In this perspective piece, we trace current challenges surrounding the appropriate development and clinical application of PRS in diverse patient cohorts to ongoing difficulties deciding which facets of population structure matter, and for what reasons, to human health. Despite numerous analytical innovations, there are reasons that emerge from Lewontin's work to remain sceptical that accounting for population structure in the context of polygenic risk estimation will allow us to more effectively identify and intervene on the significant health disparities which plague marginalized populations around the world.This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
A comprehensive study of mRNA and long noncoding RNAs in Indian Breast cancer patients using transcriptomics approach
Authors: Manjunath Meghana , Nirgude Snehal , Mhatre Anisha , Gayatri Sai Vemuri , Nataraj Mallika , Thumsi Jayanti , choudhary Bibha 
Published: April 2022

AbstractBackgroundBreast cancer (BC) is one of the leading causes of cancer-associated death in women. Despite the progress in therapeutic regimen, resistance and recurrence of Breast cancer have impacted Overall Survival. Transcriptomic profiling of tumour samples has led to identifying subtype-specific differences, identifying biomarkers, and designing therapeutic strategies. Although there are multiple transcriptomic studies on breast cancer patients from different geographical regions, a comprehensive study on long noncoding RNA (lncRNA) and mRNA in Indian Breast cancer patients in multiple subtypes are very limited. This study aims to understand the subtype-specific alterations and mRNA-lncRNA gene sets.MethodWe have performed transcriptome analysis of 17 Indian breast cancer patients and matched normal belonging to 6 different subtypes, i.e., four patients in triple positive, three patients in estrogen receptor-positive (ER+ve), three patients in estrogen and progesterone receptor-positive (ER+ve, PR+ve), two patients in Human epidermal growth factor receptor (Her2+ve), three patients in triple-negative and one patient in ER+ve and Her2 +ve subtypes. Hierarchical clustering and principal component analysis were performed using R packages to derive gene sets. Univariate and multivariate Cox analyses were performed for survival analysis.ResultsmRNA and lncRNA expression profiles segregated Indian Breast cancer subtypes with minimum overlap. We have identified a 25mRNA-27 lncRNA gene set, which displayed proper segregation of the subtypes in our data. The same gene set also segregated premenopausal women samples in The Cancer Genome Atlas (TCGA) data. Pathway analysis of the differentially expressed genes revealed unique pathways for premenopausal and postmenopausal women. Kaplan-Meier survival analysis revealed menopausal status, grade of the tumour, and hormonal status displayed statistically significant effects (p < 0.05) on the risk of mortality due to breast cancer. Her2+ve patients showed low overall survivalConclusionThis is the first study describing subtype-specific mRNA and lncRNA gene expression in Indian Breast Cancer patients with unique pathway signatures for premenopausal and postmenopausal breast cancer patients. Additionally, our data identified an mRNA-lncRNA gene set that could segregate pre and postmenopausal women with Breast Cancer. Although the sample size is small, results from this study could be a foundation that could be validated further in a larger dataset to establish an mRNA-lncRNA signature specific to the Indian population which might, in turn, improve therapeutic decisions.
The Decision of the Optimal Rank of a Non-negative Matrix Factorization Model for Gene Expression Datasets Utilizing Unit Invariant Knee Method
Authors: Güven Emine 
Published: April 2022

AbstractBackgroundThere is a great need to develop a computational approach to analyze and exploit the information contained in gene expression data. Recent utilization of non-negative matrix factorization (NMF) in computational biology has served its capability to derive essential details from a high amount of data in particular gene expression microarrays.ObjectiveA common problem in NMF is finding the proper number rank (r) of factors. Thus, various techniques have been suggested to select the optimal value of rank factorization (r).MethodThis study focused on the unit invariant knee (UIK) method to calculate factorization rank (basis vector) of the non-negative matrix factorization (NMF) of gene expression data sets is employed. Because the UIK method requires an extremum distance estimator (EDE) that is eventually employed for inflection and identification of a knee point, this study finds the first inflection point of curvature of RSS of the proposed algorithms using the UIK method on gene expression datasets as a target matrix.ResultsComputation was conducted for the UIK task using the esGolub data set of R studio, and consequently, the distinct results of NMF was subjected to compare on different algorithms. The proposed UIK method is easy to perform, free of a priori rank value input, and does not require initial parameters that significantly influence the model’s functionality.ConclusionThis study demonstrates that the UIK method provides a credible prediction for both gene expression data and precisely estimating of simulated mutational processes data with known dimensions.