bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic, fibrotic and splicing pathways are all altered in Emery-Dreifuss muscular dystrophy spectrum patients to differing degrees
Authors: de las Heras Jose I , Todorow Vanessa , Krečinić-Balić Lejla , Hintze Stefan , Czapiewski Rafal , Webb Shaun , Schoser Benedikt , Meinke Peter , Schirmer Eric C 
Published: October 2022

AbstractEmery-Dreifuss muscular dystrophy (EDMD) is a genetically and clinically variable disorder. Previous attempts to use gene expression changes to find its pathomechanism were unavailing, so we engaged a functional pathway analysis. RNA-Seq was performed on cells from 10 patients diagnosed with an EDMD spectrum disease with different mutations in seven genes. Upon comparing to controls, the pathway analysis revealed that multiple genes involved in fibrosis, metabolism, myogenic signaling and splicing were affected in all patients. Splice variant analysis revealed alterations of muscle-specific variants for several important muscle genes. Deeper analysis of metabolic pathways revealed a reduction in glycolytic and oxidative metabolism and reduced numbers of mitochondria across a larger set of 14 EDMD spectrum patients and 7 controls. Intriguingly, the gene expression signatures segregated the patients into three subgroups whose distinctions could potentially relate to differences in clinical presentation. Finally, differential expression analysis of miRNAs changing in the patients similarly highlighted fibrosis, metabolism and myogenic signaling pathways. This pathway approach revealed a transcriptome profile that can both be used as a template for establishing a biomarker panel for EDMD and direct further investigation into its pathomechanism. Furthermore, the segregation of specific gene changes into distinct groups that appear to correlate with clinical presentation may template development of prognostic biomarkers, though this will first require their testing in a wider set of patients with more clinical information.
A mutation inATP11Acauses autosomal-dominant auditory neuropathy type 2
Authors: Chepurwar Shashank , von Loh Sarah M , Wigger Daniela C , Neef Jakob , Frommolt Peter , Beutner Dirk , Lang-Roth Ruth , Kubisch Christian , Strenzke Nicola , Volk Alexander E 
Published: October 2022

AbstractAuditory synaptopathy/neuropathy (AS/AN) is a distinct type of sensorineural hearing loss in which the cochlear sensitivity to sound (i.e. active cochlear amplification by outer hair cells) is preserved whereas sound encoding by inner hair cells and/or auditory nerve fibers is disrupted owing to genetic or environmental factors. Autosomal-dominant auditory neuropathy type 2 (AUNA2) was linked either to chromosomal bands 12q24 or 13q34 in a large German family in 2017. By whole-genome sequencing, we now detected a 5500 bp deletion in ATP11A on chromosome 13q34 segregating with the phenotype in this family. ATP11A encodes a P-type ATPase that translocates phospholipids from the exoplasmic to the cytoplasmic leaflet of the plasma membrane. The deletion affects both isoforms of ATP11A and activates a cryptic splice site leading to the formation of an alternative last exon. ATP11A carrying the altered C-terminus loses its flippase activity for phosphatidylserine. Atp11a is expressed in fibers and synaptic contacts of the auditory nerve and in the cochlear nucleus in mice, and conditional Atp11a knockout mice show a progressive reduction of the spiral ganglion neuron compound action potential, recapitulating the human phenotype of AN. By combining whole-genome sequencing, immunohistochemistry, in vitro functional assays and generation of a mouse model, we could thus identify a partial deletion of ATP11A as the genetic cause of AUNA2.
Development and validation of questionnaire assessing the perception of hospital patient safety practices in public health facilities of India
Authors: Krishnamoorthy Yuvaraj , Samuel Gerald , Elangovan Venmathi , Kanth Krishna , Krishnan Murali , Sinha Isha 
Published: October 2022

AbstractBackgroundIn ‘To Err is Human’ released by the Institute of Medicine Committee on Quality of Health Care, it was emphasized that it is important to establish a safety culture in the hospitals and ensure that patients are not inadvertently harmed by errors.ObjectiveHence, we developed and validated a questionnaire for assessing the perception of patient safety practices across secondary and tertiary care facilities in India.MethodThe scale was developed based on the literature review and expert opinion. It consisted of 10 questions, and the responses to these items were based on a five-point Likert scale ranging from ‘strongly agree’ to ‘strongly disagree’. All analysis was performed using STATA version 14.2 software. Exploratory factor analysis (EFA) was run using principal component analysis with oblique promax rotation and confirmatory factor analysis (CFA) using structural equation modelling with maximum likelihood estimation.ResultsThe entire dataset was split into testing set to run EFA (with 692 participants) and validation set to run CFA (with 645 participants). In EFA, two factors were retained as they had eigenvalue more than one (4.76, 1.09) and the scree plot also showed that the slope flattens off after two factors. Factor loadings were generated using oblique promax rotation. Factor 1 consisted of seven items (Item 1, Item 2, Item 3, Item 4, Item 5, Item 6 and Item 7—questions related to patient–doctor communication, hospital environment and procedures) accounting for 47.6% of variance, and Factor 2 had three items (Item 8, Item 9 and Item 10—infection prevention and control practices in hospital) explaining 10.9% of the variance. Thus, together, the two factors explained 58.5% of the variance. CFA revealed good confirmatory fit indices of 0.85, standardized root mean square residual of 0.07 and acceptable Tucker-Lewis Index of 0.80. The reliability coefficient was 0.88 indicating very good internal consistency.ConclusionThis study develops and validates a scale that can be used universally for assessing the patients’ perception on hospital safety practices across secondary and tertiary care facilities in India.
A historical perspective on diversity in Clinical Laboratory Sciences Programs
Authors: Ahamad Afrinash , Guglielmo Jeannie 
Published: October 2022

Abstract

Objective
Diversity is integral for an effective learning environment and pedagogy. In this study, we aim to determine the student and faculty diversity in the Clinical Laboratory Sciences programs at Stony Brook University.

Methods
We retrospectively analyzed data over 20 years for the traditional program and 8 years for the hybrid program.

Results
Over 20 years, 502 students graduated from the traditional program, and 96 students graduated from the hybrid program. In the traditional program, an average of 25 students enrolled with 75% female and 25% male and in the hybrid program, an average of 12 students with 8.5 female and 3.5 male enrolled. The traditional program had the highest proportion of Asian students (50%), with White students making up 24.5%, whereas the highest proportions in the hybrid program were 35% White students and 24% Hispanic students. Among the 5 boroughs of New York City, the highest proportion of student representation was from Queens and Manhattan in both traditional (24.1%) and hybrid programs (16.7%). There were 30% male and 70% female faculty served in the traditional program whereas the current representation of fulltime faculty is 100% female.

Conclusion
Our data show the diversity of students and faculty in clinical laboratory sciences programs at Stony Brook University institution.
Association of CEA, NSE, CYFRA 21-1, SCC-Ag, and ProGRP with Clinicopathological Characteristics and Chemotherapeutic Outcomes of Lung Cancer
Authors: Bi Huijuan , Yin Lina , Fang Wenhao , Song Shenglan , Wu Shan , Shen Jilu 
Published: October 2022

Abstract

Objective
The aim of this study was to investigate the association of serum carcinoembryonic antigen (CEA), nerve-specific enolase (NSE), cytokeratin 19 fragment (CYFRA21-1), squamous cell carcinoma antigen (SCC-Ag), and pro-gastrin-releasing peptide (ProGRP) with the clinicopathological characteristics and chemotherapeutic outcomes of patients with lung cancer.

Methods
A total of 189 patients with lung cancer (lung cancer group) diagnosed at the Fourth Affiliated Hospital of Anhui Medical University from January 2020 to December 2021 were included. During the same period, 199 patients with benign lung disorders were included as the benign lung disease group and 75 healthy people were selected as the control group. The serum concentrations of CEA, NSE, CYFRA21-1, SCC-Ag, and ProGRP in all the 3 groups were analyzed and compared in patients with different lung cancer tumor-node-metastasis (TNM) stages and pathological classifications. A total of 11 patients with small cell lung cancer (SCLC) and 18 patients with lung adenocarcinoma (LAC) were further evaluated for the dynamic changes of CEA, NSE, CYFRA21-1, SCC-Ag, and ProGRP before chemotherapy and during the 6 courses of chemotherapy, and the outcome of chemotherapy was evaluated every 2 courses.

Results
The serum concentrations of CEA, NSE, CYFRA21-1, SCC-Ag, and ProGRP in the lung cancer group were significantly higher than those in the control group (P &lt; .05). We found statistically significant differences in serum CEA, NSE, CYFRA 21-1, SCC-Ag, and ProGRP among patients with different pathological types (LAC, squamous cell carcinoma, or SCLC) and different stages (I–IV). The ProGRP and NSE had the highest expression in SCLC, CEA showed the highest expression in LAC, whereas CYFRA21-1 and SCC-Ag showed the highest expression in lung squamous cell carcinoma (LSCC). The concentrations of all the markers were elevated in the advanced pathological stages. The receiver operating characteristic curve analysis showed that the diagnostic value of the combined detection of CEA, NSE, CYFRA 21-1, SCC-Ag, and ProGRP for lung cancer was significantly higher than using a single biomarker (P &lt; .05). Our dynamic monitoring results show that ProGRP progressively decreased in remission cases of SCLC and CEA progressively decreased in LAC remission cases.

Conclusion
CEA, NSE, CYFRA 21-1, SCC-Ag, and ProGRP have good clinical value in the early diagnosis, differential diagnosis, and progression monitoring of lung cancer. The ProGRP and CEA concentrations are beneficial for evaluating the outcome of chemotherapy in SCLC and LAC. The combined detection of multiple biomarkers shows improved clinical value in the early diagnosis of lung cancer.
An extended [C ii] halo around a massive star-forming galaxy at z = 5.3
Authors: Lambert Trystan S , Posses A , Aravena M , Gónzalez-López J , Assef R J , Díaz-Santos T , Brisbin D , Decarli R , Herrera-Camus R , Mejía J , Ricci C 
Published: October 2022

ABSTRACT
High-redshift observations are often biased towards massive and bright galaxies that are not necessarily representative of the full population. In order to accurately study galaxy evolution and mass assembly at these redshifts, observations of ‘normal’ main sequence galaxies are required. Here we present Atacama Large Millimeter/Submillimeter Array (ALMA) 0.3 arcsec resolution observations of the [C ii] emission line at 158 μm of HZ7, a main sequence galaxy at z = 5.25. Comparing to archival rest-frame UV observations taken by the Hubble Space Telescope (HST), we find strong evidence of the existence of extended [C ii] emission, which we estimate to be twice the size of the rest-frame UV emission, yielding one of the first high-redshift objects where a clear signature of a [C ii] ‘Halo’ has been detected to date. For a matched Sérsic profile with n = 1, we measured a [C ii] effective radius of 0.50 ± 0.04 arcsec (3.07 ± 0.25 kpc) and an average rest-frame UV effective radius of 0.2 ± 0.04 arcsec (1.48 ± 0.16 kpc). The [C ii] morphology and kinematics of the system suggest a merging event resulting in a non-rotating disc system. This event could be responsible for the extended [CII] emission. Alternatively, some potential obscured emission could also explain the [C ii] to UV size ratio. These results contribute to the growing consensus with respect to the existence of extended [C ii] emission around galaxies.
The REBELS ALMA Survey: efficient Ly α transmission of UV-bright z ≃ 7 galaxies from large velocity offsets and broad line widths
Authors: Endsley Ryan , Stark Daniel P , Bouwens Rychard J , Schouws Sander , Smit Renske , Stefanon Mauro , Inami Hanae , Bowler Rebecca A A , Oesch Pascal , Gonzalez Valentino , Aravena Manuel , da Cunha Elisabete , Dayal Pratika , Ferrara Andrea , Graziani Luca , Nanayakkara Themiya , Pallottini Andrea , Schneider Raffaella , Sommovigo Laura , Topping Michael , van der Werf Paul , Hutter Anne 
Published: October 2022

ABSTRACT
Recent work has shown that UV-luminous reionization-era galaxies often exhibit strong Lyman-alpha emission despite being situated at redshifts where the IGM is thought to be substantially neutral. It has been argued that this enhanced Ly α transmission reflects the presence of massive galaxies in overdense regions which power large ionized bubbles. An alternative explanation is that massive galaxies shift more of their Ly α profile to large velocities (relative to the systemic redshift) where the IGM damping wing absorption is reduced. Such a mass-dependent trend is seen at lower redshifts, but whether one exists at z ∼ 7 remains unclear owing to the small number of existing systemic redshift measurements in the reionization era. This is now changing with the emergence of [C ii]-based redshifts from ALMA. Here, we report MMT/Binospec Ly α spectroscopy of eight UV-bright (MUV ∼ −22) galaxies at z ≃ 7 selected from the ALMA REBELS survey. We detect Ly α in four of eight galaxies and use the [C ii] systemic redshifts to investigate the Ly α velocity profiles. The Ly α lines are significantly redshifted from systemic (average velocity offset = 223 km s–1) and broad (FWHM ≈ 300–650 km s−1), with two sources showing emission extending to ≈750 km s−1. We find that the broadest Ly α profiles are associated with the largest [C ii] line widths, suggesting a potential link between the Ly α FWHM and the dynamical mass. Since Ly α photons at high velocities transmit efficiently through the z = 7 IGM, our data suggest that velocity profiles play a significant role in boosting the Ly α visibility of the most UV-luminous reionization-era galaxies.
An Approximate Bayesian Computation Approach for Modeling Genome Rearrangements
Authors: Moshe Asher , Wygoda Elya , Ecker Noa , Loewenthal Gil , Avram Oren , Israeli Omer , Hazkani-Covo Einat , Pe’er Itsik , Pupko Tal 
Published: October 2022

AbstractThe inference of genome rearrangement events has been extensively studied, as they play a major role in molecular evolution. However, probabilistic evolutionary models that explicitly imitate the evolutionary dynamics of such events, as well as methods to infer model parameters, are yet to be fully utilized. Here, we developed a probabilistic approach to infer genome rearrangement rate parameters using an Approximate Bayesian Computation (ABC) framework. We developed two genome rearrangement models, a basic model, which accounts for genomic changes in gene order, and a more sophisticated one which also accounts for changes in chromosome number. We characterized the ABC inference accuracy using simulations and applied our methodology to both prokaryotic and eukaryotic empirical datasets. Knowledge of genome-rearrangement rates can help elucidate their role in evolution as well as help simulate genomes with evolutionary dynamics that reflect empirical genomes.
Archaeology and Material Culture of the Kingdom of Israel and the Israelites (C. 1000 – 722/21 BCE)
Authors: Greer Jonathan S. 
Published: October 2022

Biblical texts describe the foundation of the kingdom of Israel (also known as the “northern kingdom”) as a secession, in which the northern tribes revolted against the installation of Rehoboam son of Solomon and appointed Jeroboam son of Nebat as their king (1 Kgs 12). The resultant kingdom of Israel is described as enduring for some two hundred years reigned by twenty kings from nine dynastic houses (though some “dynasties” are only represented by ephemeral reigns of a single king), a portrayal broadly corroborated by ancient inscriptions, Neo-Assyrian annals, and archaeology for the later 9th and 8th centuries bce, though archaeological debate surrounds the origins of the kingdom. Its end was ushered in by the devastating 733–732 bce campaigns of Tiglath-Pileser III that resulted in the annexation of the Upper Galilee, with the final blow coming in 722 or 721 in the conquest of the capital of Samaria following a siege by Shalmanesser V and then Sargon II. The geographical boundaries of the region are described in the Hebrew Bible in terms of cities affiliated with varying degrees of centralization and those boundaries fluctuated some throughout the period. The extent of the kingdom at any given time is difficult to identify archaeologically, but the heartland of the northern central hills remained stable as the capital moved from Shechem to Tirzah and eventually to Samaria under the Omrides (cf. 1 Kgs 12:25; 15:33; 16:24). The kingdom reached its first peak of power and broad geographic extent under the Omrides encompassing the Galilee, the Sharon plain, the Jezreel Valley, and the Jordan Valley as well as regions of the Transjordan. There is also biblical and extrabiblical evidence for northern control of southern regions as far as the Gulf of Aqaba that would have included important caravan routes through the Sinai. Archaeological surveys and site excavations demonstrate the regional prominence of the kingdom, although debate remains regarding the appearance of monumental architecture and other material remains as part of a larger discussion surrounding the end of the Iron Age I and the beginning of the Iron Age II. Expansion under the Omrides in the 9th century bce brought the kingdom into conflict with other regional kingdoms and the Neo-Assyrian empire, as attested in a number of significant epigraphic discoveries including the Moabite Mesha stela, the Aramean Tel Dan stela, and many neo-Assyrian inscriptions. A second and perhaps more expansive peak of power occurred under the Nimshides in the 8th century bce, especially during the reign of Jeroboam II, due to the Neo-Assyrian domination of the rival kingdom of Aram Damascus before Assyria set its sights on Samaria. Archaeological discoveries have also shed light on the wealth and economy of the Israelite kingdom and have proved essential in reconstructing religious practices, social structures, and the activities of everyday life.
Cytosolic disproportionating enzyme2 is essential for pollen germination and pollen tube elongation in rice
Authors: Chen Liangke , Dong Xiangbai , Yang Huifang , Chai Yaru , Xia Yan , Tian Lihong , Qu Le Qing 
Published: October 2022

Abstract
Degradation of starch accumulated in pollen provides energy and cellular materials for pollen germination and pollen tube elongation. Little is known about the function of cytosolic disproportionating enzyme2 (DPE2) in rice (Oryza sativa). Here, we obtained several DPE2 knockout mutant (dpe2) lines via genomic editing and found that the mutants grew and developed normally but with greatly reduced seed-setting rates. Reciprocal crosses between dpe2 and wild-type plants demonstrated that the mutant was male sterile. In vitro and in vivo examinations revealed that the pollen of the dpe2 mutant developed and matured normally but was defective in germination and elongation. DPE2 deficiency increased maltose content in pollen, whereas it reduced the levels of starch, glucose, fructose, and adenosine triphosphate (ATP). Exogenous supply of glucose or ATP to the germination medium partially rescued the pollen germination defects of dpe2. The expression of cytosolic phosphorylase2 (Pho2) increased significantly in dpe2 pollen. Knockout of Pho2 resulted in a semi-sterile phenotype. We failed to obtain homozygous dpe2 pho2 double mutant lines. Our results demonstrate that maltose catalyzed by DPE2 to glucose is the main energy source for pollen germination and pollen tube elongation, while Pho2 might partially compensate for deficiency of DPE2.
Predicting vigilance vulnerability during 1 and 2 weeks of sleep restriction with baseline performance metrics
Authors: Lo June C , Ang Jit Wei A , Koa Tiffany B , Ong Ju Lynn , Lim Julian 
Published: October 2022

AbstractStudy ObjectivesWe attempted to predict vigilance performance in adolescents during partial sleep deprivation using task summary metrics and drift diffusion modelling measures (DDM) derived from baseline vigilance performance.MethodsIn the Need for Sleep studies, 57 adolescents (age = 15–19 years) underwent two baseline nights of 9-h time-in-bed (TIB), followed by two cycles of weekday sleep-restricted nights (5-h or 6.5-h TIB) and weekend recovery nights (9-h TIB). Vigilance was assessed daily with the Psychomotor Vigilance Task (PVT), with the number of lapses (response times ≥ 500 ms) as the primary outcome measure. The two DDM predictors were drift rate, which quantifies the speed of information accumulation and determines how quickly an individual derives a decision response, and non-decision time range, which indicates within-subject variation in physical, non-cognitive responding, e.g. motor actions.ResultsIn the first week of sleep curtailment, faster accumulation of lapses was significantly associated with more lapses at baseline (p = .02), but not the two baseline DDM metrics: drift and non-decision time range (p &gt; .07). On the other hand, faster accumulation of lapses and greater increment in reaction time variability from the first to the second week of sleep restriction were associated with lower drift (p &lt; .007) at baseline.ConclusionsAmong adolescents, baseline PVT lapses can predict inter-individual differences in vigilance vulnerability during 1 week of sleep restriction on weekdays, while drift more consistently predicts vulnerability during more weeks of sleep curtailment.Clinical Trial InformationEffects of Napping in Sleep-Restricted Adolescents, clinicaltrials.gov, NCT02838095. The Cognitive and Metabolic Effects of Sleep Restriction in Adolescents (NFS4), clinicaltrials.gov, NCT03333512.
Small islands and large biogeographic barriers have driven contrasting speciation patterns in Indo-Pacific sunbirds (Aves: Nectariniidae)
Authors: Ó Marcaigh Fionn , Kelly David J , O’Connell Darren P , Analuddin Kangkuso , Karya Adi , McCloughan Jennifer , Tolan Ellen , Lawless Naomi , Marples Nicola M 
Published: October 2022

AbstractBirds of the Indo-Pacific have provided biologists with many foundational insights. This study presents evidence for strong phylogeographic structure in two sunbird species from the heart of this region, the olive-backed sunbird, Cinnyris jugularis, and the black sunbird, Leptocoma aspasia. We assessed population divergence using morphological, plumage, bioacoustic and molecular data (mitochondrial ND2/ND3). Our findings indicate that the olive-backed sunbird should be recognized as multiple species, because birds from Sulawesi and the Sahul Shelf are closely related to each other, but widely separated from those in other regions. In addition, we provide evidence for an endemic species on the Wakatobi Islands, an archipelago of deep-sea islands off south-east Sulawesi. That a small bird could exhibit a range all the way from Sulawesi to Australia, while diverging on a small archipelago within this range, illustrates the complex interplay between dispersal and speciation. Our black sunbird genetic data also suggest unrecognized population structure, despite relatively weak plumage divergence. Black sunbirds in Sulawesi are likely to be a separate species from those in New Guinea, with a mean genetic distance of 9.1%. Current taxonomy suggests these sunbird species transcend classic biogeographic barriers, but our results suggest that these barriers are not easily bypassed.