bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Gladiator's Tears: Epiphora From Ancient Rome
Authors: Galassi Francesco M. , Habicht Michael E. , Killgrove Kristina , De Carolis Stefano , Polidoro Massimo , Haeusler Martin 
Published: September 2019

Abstract
This article examines the clinical presentation of epiphora in Ancient Rome through the historico-medical analysis of the literary evidence provided by the verses by the poet Juvenal in his Satire VI. A gladiator's ophthalmological problem is interpreted as epiphora caused by traumatic injuries to the craniofacial region, compatible with those described in the palaeopathological literature. This analysis also focuses on the history of epiphora in antiquity and its treatment.
Three-Dimensional Analysis of Cortical Bone Thickness in Individuals With Non-Syndromic Unilateral Cleft Lip and Palate
Authors: Ko Jaemin , Han Hae Jin , Hoffman William , Oberoi Snehlata 
Published: September 2019

Purpose:
The aim of this study was to measure the cortical bone thickness of the infrazygomatic crest area in individuals with unilateral cleft lip and palate using cone beam computed tomography for placement of miniplates used for bone anchored maxillary protraction.

Materials and Methods:
CBCT scans were obtained from 31 non-syndromic UCLP children diagnosed with maxillary hypoplasia (17 males, 14 females, mean age: 11.9 years). 5 horizontal and 5 vertical reference planes were drawn at the infrazygomatic crest area. The cortical bone thickness at 25 intersection points on the cleft side and the non-cleft side was measured.

Results:
The mean cortical bone thickness of the 25 measured points was 1.19 mm on the cleft side and 1.17 mm on the non-cleft side with no significant difference. The greatest cortical bone thickness was found to be at the most superior, posterior point (H+6, V+0), which was 1.49 mm on the cleft side and 1.47 mm on the non-cleft side. The thinnest mean cortical bone thickness was measured at the most inferior, anterior point (H−2, V−8), which was 0.94 mm on the cleft side and 0.95 mm on the non-cleft side. There was no significant difference between males and females.
Experience of Replantation and Reconstruction in Total Scalp, Partial Forehead, and Ear Avulsions
Authors: Dadaci Mehmet , Yildirim Mehmet Emin Cem , Ince Bilsev 
Published: September 2019

Abstract
In this study, the authors present the challenges of replantation and management of 2 patients who have total scalp, partial forehead and ear avulsion. A 39-year-old male farmer was admitted to the emergency room with the total scalp, forehead, partial right eyebrow and upper eyelid amputation after his hair was catched by an agricultural machine. Anastomoses of 2 arteries and 2 veins in the occipital region were done first. Anastomosis of the right and left superficial temporal arteries and veins were performed end to end by turning the operating table without moving the head, followed by 1 vein anastomoses in the frontal region. Although anastomotic blood flow was observed by Doppler ultrasonography, there were changes suggesting necrosis in the frontal and both temporoparietal regions and later in the occipital region. Necrotic tissues began to be debrided tangentially from the 10th day. During serial debridement, it was observed that the necrotic tissue includes skin and connective tissue. At the end of the post-operative second month, surgical treatment was completed and 12 months after the surgery, the patient lives with the wig because of hair loss, but the patient is cosmetically satisfied. An 18-year-old female gatherer was admitted to the emergency room with the total scalp, both eyebrows, right upper eyelid and partial right ear avulsion, after her hair was catched by an agricultural machine. Totally, anastomoses of 4 arteries and 3 veins were performed. On the 10th post-operative day, necrotic skin findings appeared and serial debridement were performed and it was revealed that aponeurosis was fully intact. The defect areas of skin and connective tissue were repaired with STSG. Intact partial temporal scalp tissue was present. Scalp replantation should always be considered as the first choice, according to the similar tissue principle of tissue repair in plastic surgery if there is no contraindication. Additionally, performing multiple arterial and vein anastomoses, evaluating the patient position in the post-operative period for anastomosis and hemodynamic follow-up, avoiding aggressive debridement and early reconstruction may give the patient the chance of skin grafting which is the basis of the reconstructive ladder.
Rise and Regional Disparities in Buprenorphine Utilization in the United States
Authors: Pashmineh Amir Azar R. , Cruz-Mullane Alexandra , Podd Jaclyn C. , Lam Warren S. , Kaleem Suhail H. , Lockard Laura B. , Mandel Mark R. , Chung Daniel Y. , Davis Corey S. , Nichols Stephanie D. , McCall Kenneth L. , Piper Brian J. 
Published: September 2019

AbstractAimsBuprenorphine is an opioid partial-agonist used to treat Opioid Use Disorders (OUD). While several state and federal policy changes have attempted to increase buprenorphine availability, access remains well below optimal levels. This study characterized how buprenorphine utilization in the United States has changed over time and whether there are regional disparities in distribution.MeasurementsBuprenorphine weights distributed from 2007 to 2017 were obtained from the Drug Enforcement Administration. Data was expressed as the percent change and as the mg per person in each state. Separately, the formulations for prescriptions covered by Medicaid (2008 to 2018) were examined.FindingsBuprenorphine distributed to pharmacies increased about seven-fold (476.8 to 3,179.9 kg) while the quantities distributed to hospitals grew five-fold (18.6 to 97.6 kg) nationally from 2007 to 2017. Buprenorphine distribution per person was almost 20-fold higher in Vermont (40.4 mg/person) relative to South Dakota (2.1 mg/person). There was a strong association between the number of waivered physicians per 100K population and distribution per state (r(49) = +0.76, p < .0005). The buprenorphine/naloxone sublingual film (Suboxone) was the predominant formulation (92.6% of 0.31 million Medicaid prescriptions) in 2008 but this accounted for less than three-fifths (57.3% of 6.56 million prescriptions) in 2018.ConclusionsAlthough buprenorphine availability has substantially increased over the last decade, distribution was very non-homogenous across the US.
Electrophysiological network alterations in adults with copy number variants associated with high neurodevelopmental risk
Authors: Dima Diana C. , Adams Rachael , Linden Stefanie C. , Baird Alister , Smith Jacqueline , Foley Sonya , Perry Gavin , Routley Bethany C. , Magazzini Lorenzo , Drakesmith Mark , Williams Nigel , Doherty Joanne , van den Bree Marianne B.M. , Owen Michael J. , Hall Jeremy , Linden David E. J. , Singh Krish D. 
Published: September 2019

AbstractRare copy number variants associated with increased risk for neurodevelopmental and psychiatric disorders (referred to as ND-CNVs) are characterized by heterogeneous phenotypes thought to share a considerable degree of overlap. Altered neural integration has often been linked to psychopathology and is a candidate marker for potential convergent mechanisms through which ND-CNVs modify risk; however, the rarity of ND-CNVs means that few studies have assessed their neural correlates. Here, we used magnetoencephalography (MEG) to investigate resting-state oscillatory connectivity in a cohort of 42 adults with ND-CNVs, including deletions or duplications at 22q11.2, 15q11.2, 15q13.3, 16p11.2, 17q12, 1q21.1, 3q29, and 2p16.3, and 42 controls. We observed decreased connectivity between occipital, temporal and parietal areas in participants with ND-CNVs. This pattern was common across genotypes and not exclusively characteristic of 22q11.2 deletions, which were present in a third of our cohort. Furthermore, a data-driven graph theory framework enabled us to successfully distinguish participants with ND-CNVs from unaffected controls using differences in node centrality and network segregation. Together, our results point to alterations in electrophysiological connectivity as a putative common mechanism through which genetic factors confer increased risk for neurodevelopmental and psychiatric disorders.
OmicsX: a web server for integrated OMICS analysis
Authors: Pan Jianbo , Qian Jiang , Zhang Hui 
Published: September 2019

ABSTRACTHigh-throughput omic data sets like genomics, transcriptomics, proteomics, glycomics, lipitomics, metabolomics, and modified forms of the biological molecules have been generated to investigate biological mechanisms. Accordingly, bioinformatic methods and tools have been developed and applied to analyze the omics data for different purposes. However, a lack of comparison and integration tools impedes the deep exploration of multi-omics data. OmicsX is a user-friendly web server for integration and comparison of different omic datasets with optional sample annotation information. The tool includes modules for gene-wise correlation, sample-wise correlation, subtype clustering, and differential expression. OmicsX provides researchers the analysis results with visualization, searching, and data downloading, and help to suggest the biological indications from the comparison of different omic data.Availability and implementationhttp://bioinfo.wilmer.jhu.edu/OmicsX/
The scale-invariant, temporal profile of neuronal avalanches in relation to cortical γ–oscillations
Authors: Miller Stephanie R. , Yu Shan , Plenz Dietmar 
Published: September 2019

ABSTRACTActivity cascades are found in many complex systems. In the cortex, they arise in the form of neuronal avalanches that capture ongoing and evoked neuronal activities at many spatial and temporal scales. The scale-invariant nature of avalanches suggests that the brain is in a critical state, yet predictions from critical theory on the temporal unfolding of avalanches have yet to be confirmed in vivo. Here we show in awake nonhuman primates that the temporal profile of avalanches follows a symmetrical, inverted parabola spanning up to hundreds of milliseconds. This parabola constrains how avalanches initiate locally, extend spatially and shrink as they evolve in time. Importantly, parabolas of different durations can be collapsed with a scaling exponent close to 2 supporting critical generational models of neuronal avalanches. Spontaneously emerging, transient γ–oscillations coexist with and modulate these avalanche parabolas thereby providing a temporal segmentation to inherently scale-invariant, critical dynamics. Our results identify avalanches and oscillations as dual principles in the temporal organization of brain activity.Significance StatementThe most common framework for understanding the temporal organization of brain activity is that of oscillations, or ‘brain waves’. In oscillations, distinct physiological frequencies emerge at well-defined temporal scales, dividing brain activity into time segments underlying cortex function. Here, we identify a fundamentally different temporal parsing of activity in cortex. In awake Macaque monkeys, we demonstrate the motif of an inverted parabola that governs the temporal unfolding of brain activity in the form of neuronal avalanches. This symmetrical motif is scale-invariant, that is, it is not tied to time segments, and exhibits a scaling exponent close to 2, in line with prediction from theory of critical systems. We suggest that oscillations provide a transient regularity in an otherwise scale-invariant temporal organization pervading cortical activity at numerous scales.
An improved Xer-cise technology for the generation of multiple unmarked mutants in Mycobacteria
Authors: Boudehen Yves-Marie , Wallat Maximillian , Rousseau Philippe , Neyrolles Olivier , Gutierrez Claude 
Published: September 2019

SummaryXer-cise is a technique using antibiotic resistance cassettes flanked by dif sites allowing spontaneous and accurate excision from bacterial chromosomes with a high frequency through the action of the cellular recombinase XerCD. Here, we report a significant improvement of Xer-cise in Mycobacteria. Zeocin-resistance cassettes flanked by variants of the natural Mycobacterium tuberculosis dif site were constructed and shown to be effective tools to construct multiple unmarked mutations in M. tuberculosis and in the model species Mycobacterium smegmatis. The dif site variants harbor mutations in the central region and can therefore not recombine with the wild type or other variants, resulting in mutants of increased genetic stability. The herein described method should be generalizable to virtually any transformable bacterial species.Method summarydif-ZeoR-dif cassettes are used to replace non-essential genes in mycobacterial genome through recombineering. Spontaneous excision of the cassette is carried out under the action of the recombinase XerCD, resulting in unmarked deletions. Subsequent rounds of mutagenesis using cassettes flanked by a range of dif site variants allow construction of multiple mutants in which the different dif sites cannot recombine which each other, yielding stable genetic constructs.
ADNP promotes neural differentiation by modulating Wnt/β-catenin signaling
Authors: Sun Xiaoyun , Peng Xixia , Cao Yuqing , Zhou Yan , Sun Yuhua 
Published: September 2019

AbstractADNP (Activity Dependent Neuroprotective Protein) is proposed as a neuroprotective protein whose aberrant expression has been frequently linked to neural developmental disorders, including the Helsmoortel-Van der Aa syndrome. However, its role in neural development and pathology remains unclear. Using mESC (mouse embryonic stem cell) directional neural differentiation as a model, we show that ADNP is required for ESC neural induction and neuronal differentiation by maintaining Wnt signaling. Mechanistically, ADNP functions to maintain the proper protein levels of β-Catenin through binding to its armadillo domain which prevents its association with key components of the degradation complex: Axin and APC. Loss of ADNP promotes the formation of the degradation complex and hyperphosphorylation of β-Catenin by GSK3β and subsequent degradation via ubiquitin-proteasome pathway, resulting in down-regulation of key neuroectoderm developmental genes. We further show that ADNP plays key role in cerebellar neuron formation. Finally, adnp gene disruption in zebrafish embryos recapitulates key features of the mouse phenotype, including the reduced Wnt signaling, defective embryonic cerebral neuron formation and the massive neuron death. Thus, our work provides important insights into the role of ADNP in neural development and the pathology of the Helsmoortel-Van der Aa syndrome caused by ADNP gene mutation.
AFM based elasticity of intestinal epithelium correlate with barrier function under drug action
Authors: Tejeda-Mora H. , Stevens L. , Gröllers M. , Katan A. , van de Steeg E. , van der Heiden M. 
Published: September 2019

ABSTRACTOver the past few years, atomic force microscopy (AFM) has developed as a mature research tool for measuring the nanomechanical properties of tissue, cells and biological structures. The force spectroscopy mode of AFM allows the local elasticity of biological samples to be measured. The mechanical properties of cells are highly affected by homeostatic changes observed during disease. In the case of the intestine, the aetiology for some conditions is still unclear. To improve the clinical translation of pre-clinical models, a new and different approach could be to study cellular behaviour in health and disease from a mechanical point of view. Specifically, knowledge of changes in epithelial membranes in response to drugs is useful for interpreting both drug action and disease development. Here, we used human intestinal Caco-2 cells as a first step to record epithelial membrane elasticity measurements at the nanoscale using AFM. Three different drugs were selected to influence intestinal epithelium integrity by specifically targeting different functional aspects of the membrane, such as permeability and support. Results indicate a relationship between measured cell elasticity and cell viability markers, such as cellular toxicity and membrane barrier functions. Our work represents a proof-of-concept that cells suffer a particular change in elastic properties depending upon the mechanism of action of an applied drug. The following may provide an efficient approach for diagnosing intestinal pathologies and testing drugs for clinical use.STATEMENT OF SIGNIFICANCEWe present evidence that epithelial membrane suffers a particular change in elastic properties depending upon the mechanism of action of an applied drug. These changes can be monitored over time using AFM technology and may provide an alternative and efficient approach for diagnosing intestinal pathologies and testing drugs for clinical use.
Ultra-Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea)
Authors: Cruaud Astrid , Delvare Gérard , Nidelet Sabine , Sauné Laure , Ratnasingham Sujeevan , Chartois Marguerite , Blaimer Bonnie B. , Gates Michael , Brady Seán G. , Faure Sariana , van Noort Simon , Rossi Jean-Pierre , Rasplus Jean-Yves 
Published: September 2019

ABSTRACTRecent technical advances combined with novel computational approaches promised the acceleration of our understanding of the tree of life. However, when it comes to hyperdiverse and poorly known groups of invertebrates, studies are still scarce. As published phylogenies will be rarely challenged by future taxonomists, careful attention must be paid to potential analytical bias. We present the first molecular phylogenetic hypothesis for the family Chalcididae, an emblematic group of parasitoid wasps, with a representative sampling (144 ingroups and 7 outgroups) that covers all described subfamilies and tribes and 82% of the known genera. Analyses of 538 Ultra-Conserved Elements (UCEs) with supermatrix (RAxML and IQTREE) and gene-tree reconciliation approaches (ASTRAL, ASTRID) resulted in highly supported topologies in overall agreement with morphology but reveal conflicting topologies for some of the deepest nodes. To resolve these conflicts, we explored the phylogenetic tree space with clustering and gene genealogy interrogation methods, analyzed marker and taxon properties that could bias inferences and performed a thorough morphological analysis (130 characters encoded for 40 taxa representative of the diversity). This joint analysis reveals that UCEs enable attainment of resolution between ancestry and convergent /divergent evolution when morphology is not informative enough, but also shows that a systematic exploration of bias with different analytical methods and a careful analysis of morphological features is required to prevent publication of artefactual results. We highlight a GC-content bias for ML approaches, an artefactual mid-point rooting of the ASTRAL tree and a deleterious effect of high percentage of missing data on gene tree reconciliation methods. Based on the results we propose a new classification of the family into eight subfamilies and 10 tribes that lay the foundation for future studies on the evolutionary history of Chalcididae.
Designing of a mini-core that effectively represents 3004 diverse accessions of rice
Authors: Kumar Angad , Kumar Shivendra , Prasad Manoj , Thakur Jitendra K. 
Published: September 2019

ABSTRACTGenetic diversity provides foundation for plant breeding and genetic research. As part of the 3K Rice Genome Project, over 3000 rice genomes were recently sequenced. We added four Indian rice accessions to it and made original panel of 3004 accessions. However, large set of germplasms are difficult to preserve and evaluate. Construction of core and mini-core collections is an efficient method for managing genetic resources. This study aims to designing of mini-core comprised of 520 accessions representing original panel. The designed mini-core captured most of the SNPs and represented all phenotypes and geographical regions. The mini-core was validated using different statistical analyses and had representation from all major groups including japonica, indica, aus/boro and aromatic/basmati. GWAS analyses with mini-core panel efficiently reproduced the marker-traits association identified among original 3004 panel. Expression analysis of trait-associated genes highlights the relevance of such mini-core panel. Haplotype analysis could also validate our mini-core panel. Apart from mini-core, we identified few regional and varietal specific marker-trait associations which were not evident in original panel. In this era of large-scale sequencing projects, such a strategy of designing mini-core will be very useful.One-sentence summaryDesigning of mini-core as manageable association panel that efficiently mirroring the large and diverse collection of 3004 rice accessions.
Physical activity and risks of breast and colorectal cancer: A Mendelian randomization analysis
Authors: Papadimitriou Nikos , Dimou Niki , Tsilidis Konstantinos K , Banbury Barbara , Martin Richard M , Lewis Sarah J , Kazmi Nabila , Robinson Timothy M , Albanes Demetrius , Aleksandrova Krasimira , Berndt Sonja I , Bishop D Timothy , Brenner Hermann , Buchanan Daniel D , Bueno-de-Mesquita Bas , Campbell Peter T , Castellví-Bel Sergi , Chan Andrew T , Chang-Claude Jenny , Ellingjord-Dale Merete , Figueiredo Jane C , Gallinger Steven J , Giles Graham G , Giovannucci Edward , Gruber Stephen B , Gsur Andrea , Hampe Jochen , Hampel Heather , Harlid Sophia , Harrison Tabitha A , Hoffmeister Michael , Hopper John L , Hsu Li , Huerta José María , Huyghe Jeroen R , Jenkins Mark A , Keku Temitope O , Kühn Tilman , Vecchia Carlo La , Marchand Loic Le , Li Christopher I , Li Li , Lindblom Annika , Lindor Noralane M , Lynch Brigid , Markowitz Sanford D , Masala Giovanna , May Anne M , Milne Roger , Monninkhof Evelyn , Moreno Lorena , Moreno Victor , Newcomb Polly A , Offit Kenneth , Perduca Vittorio , Pharoah Paul D P , Platz Elizabeth A , Potter John D , Rennert Gad , Riboli Elio , Sánchez Maria-Jose , Schmit Stephanie L , Schoen Robert E , Severi Gianluca , Sieri Sabina , Slattery Martha L , Song Mingyang , Tangen Catherine M , Thibodeau Stephen N , Travis Ruth C , Trichopoulou Antonia , Ulrich Cornelia M , van Duijnhoven Franzel JB , Van Guelpen Bethany , Vodicka Pavel , White Emily , Wolk Alicja , Woods Michael O , Wu Anna H , Peters Ulrike , Gunter Marc J , Murphy Neil 
Published: September 2019

AbstractPhysical activity has been associated with lower risks of breast and colorectal cancer in epidemiological studies; however, it is unknown if these associations are causal or confounded. In two-sample Mendelian randomization analyses, using summary genetic data from the UK Biobank and GWA consortia, we found that a one standard deviation increment in average acceleration was associated with lower risks of breast cancer (odds ratio [OR]: 0.59, 95% confidence interval [CI]: 0.42 to 0.84, P-value=0.003) and colorectal cancer (OR: 0.66, 95% CI: 0.53 to 0.82, P-value=2*E-4). We found similar magnitude inverse associations by breast cancer subtype and by colorectal cancer anatomical site. Our results support a potentially causal relationship between higher physical activity levels and lower risks of breast cancer and colorectal cancer. Based on these data, the promotion of physical activity is probably an effective strategy in the primary prevention of these commonly diagnosed cancers.DisclaimerWhere authors are identified as personnel of the International Agency for Research on Cancer / World Health Organization, the authors alone are responsible for the views expressed in this article and they do not necessarily represent the decisions, policy or views of the International Agency for Research on Cancer / World Health Organization.