bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fostering Tobacco Regulatory Team Science through a multisite, virtual fellowship program for early-career researchers
Authors: Ajayi Tinuola B. , Childs Ellen , Di Frances Remein Christy , Forbush Leigh R. , Ragasa Justin B. , Fetterman Jessica L. , Hirsch Glenn A. , Benjamin Emelia J. 
Published: January 2022

AbstractIntroduction:In an era of complex, multi-institutional, team-based science, there is little guidance for the successful creation of effective, collaborative, multisite training programs.Objective:We designed, implemented, and evaluated a multi-institutional Tobacco Regulatory Science (TRS) fellowship representing a scalable program that may be customized for other research areas.Methods:Using a mixed-methods approach, we analyzed program evaluations from trainees enrolled in the first 7 years of the American Heart Association (AHA) Tobacco Regulation and Addiction Center (A-TRAC) fellowship (2014–2021). We also reported the program outcomes, including published TRS manuscripts, independent grant funding, Food and Drug Administration (FDA) Docket comments submitted on TRS topics, TRS oral and poster presentations, research awards, and promotions in the TRS field.Results:Thirty-five unique trainees (49% [n = 17] female, 29% [n = 10] Black) from eight institutions within the A-TRAC network participated in the fellowship since its inception. The trainees reported 74 TRS publications, 78 TRS oral or poster presentations, 25 FDA Docket comment submissions, and 13 funded grant awards. Participant evaluations indicated six areas of programmatic strength: 1) blended instruction medium with webinars and in-person meetings, 2) curricular emphasis on theories of experiential learning, 3) focus on career and professional development, 4) integrated mentorship model, 5) culture of feedback and feedforward to foster successful learning, and 6) focus on recruiting diverse participants. The A-TRAC model stresses experiential education, feedback and feedforward, and peer learning.Conclusions:Our resource-effective, needs-driven program is a reproducible model for institutions interested in developing multisite, virtual research education programs in the era of team science.
Multilocus Inherited Neoplasia Allele Syndrome (MINAS): an update
Authors: McGuigan Anthony , Whitworth James , Andreou Avgi , Hearn Timothy ,   Genomics England Research Consortium, Ambrose J. C. , Arumugam P. , Bevers R. , Bleda M. , Boardman-Pretty F. , Boustred C. R. , Brittain H. , Caulfield M. J. , Chan G. C. , Fowler T. , Giess A. , Hamblin A. , Henderson S. , Hubbard T. J. P. , Jackson R. , Jones L. J. , Kasperaviciute D. , Kayikci M. , Kousathanas A. , Lahnstein L. , Leigh S. E. A. , Leong I. U. S. , Lopez F. J. , Maleady-Crowe F. , McEntagart M. , Minneci F. , Moutsianas L. , Mueller M. , Murugaesu N. , Need A. C. , O‘Donovan P. , Odhams C. A. , Patch C. , Perez-Gil D. , Pereira M. B. , Pullinger J. , Rahim T. , Rendon A. , Rogers T. , Savage K. , Sawant K. , Scott R. H. , Siddiq A. , Sieghart A. , Smith S. C. , Sosinsky A. , Stuckey A. , Tanguy M. , Taylor Tavares A. L. , Thomas E. R. A. , Thompson S. R. , Tucci A. , Welland M. J. , Williams E. , Witkowska K. , Wood S. M. , Tischkowitz Marc , Maher Eamonn R. 
Published: January 2022

AbstractMulti-locus Inherited Neoplasia Allele Syndrome (MINAS) refers to individuals with germline pathogenic variants in two or more cancer susceptibility genes(CSGs). With increased use of exome/genome sequencing it would be predicted that detection of MINAS would become more frequent. Here we review recent progress in knowledge of MINAS. A systematic literature search for reports of individuals with germline pathogenic variants in 2 or more of 94 CSGs was performed. In addition, participants with multiple primary tumours who underwent genome sequencing as part of the Rare Disease arm of the UK 100,000 Genomes Project were interrogated to detect additional cases. We identified 385 MINAS cases (211 reported in the last 5 years, 6 from 100,000 genomes participants). Most (287/385) cases contained at least one pathogenic variant in either BRCA1 or BRCA2. 108/385 MINAS cases had multiple primary tumours at presentation and a subset of cases presented unusual multiple tumour phenotypes. We conclude that, as predicted, increasing numbers of individuals with MINAS are being have been reported but, except for individuals with BRCA1/BRCA2 MINAS, individual CSG combinations are generally rare. In many cases it appears that the clinical phenotype is that which would be expected from the effects of the constituent CSG variants acting independently. However, in some instances the presence of unusual tumour phenotypes and/or multiple primary tumours suggests that there may be complex interactions between the relevant MINAS CSGs. Systematic reporting of MINAS cases in a MINAS database (e.g. https://databases.lovd.nl/shared/diseases/04296) will facilitate more accurate prognostic predictions for specific CSG combinations.
Repercussion of cAMP and EPAC in Memory and Signaling
Authors: Naz Sabreena , Mahmood Tarique , Ahsan Farogh , Rizvi Ali Abbas , Shamim Arshiya 
Published: January 2022

AbstractIt is well recognized that cyclic adenosine monophosphate (cAMP) signaling within
neurons plays a key role in the foundation of long-term memories. Memory storage
is the process that demands the movement of signals, neural plasticity, and the
molecules which can transfer the signals from the sensory neuron to the dorsal
root ganglion (DRG) neurons and later into the temporal region of the brain. The
discovery of cAMP in 1958 as the second messenger also had a role in memory
formation and other neural aspects. Further, in 1998 the scientists found that
cAMP does not just activate protein kinase A (PKA) but also exchange protein
directly activated by cAMP (Epac) which has an active role to play in
hyperalgesia, memory, and signaling. The cAMP has three targets,
hyperpolarization-activated cyclic nucleotide modulated (HCN) channels, protein
kinase A (PKA), and exchange protein activated by cAMP (Epac). Different
research has exposed that both PKA and HCN channels are significant for
long-term memory creation. Epac is a cAMP-dependent guanine nucleotide exchange
factor for the small G proteins including Rap1. However, slight information is
there about the role of Epac in this process. The effects of cAMP are
predominantly imparted by activating protein kinase A (PKA) and the more newly
discovered exchange proteins are directly activated by cAMP 1 and 2 (EPAC1 and
EPAC2). This review provides an insight regarding the function and role of both
of these secondary messengers in memory and nerve signaling.
CellCelector™ as a platform in isolating primary B cells for antibody discovery
Authors: Matochko Wadim L , Nelep Constantin , Chen Weihsu C , Grauer Stephanie , McFadden Karyn , Wilson Vicki , Oxenoid Kirill 
Published: January 2022

ABSTRACT
The most robust strategy in antibody discovery is the use of immunized animals and the ability to isolate and immortalize immune B-cells to hybridoma for further interrogation. However, capturing the full repertoire of an immunized animal is labor intensive, time consuming and limited in throughput. Therefore, techniques to directly mine the antibody repertoire of primary B-cells are of great importance in antibody discovery. In the current study, we present a method to isolate individual antigen-specific primary B-cells using the CellCellector™ single-cell isolation platform from XenoMouse® (XM) immunized with a recombinant therapeutic protein, EGFR. We screened a subset of CD138+ B-cells and identified 238 potential EGFR-specific B-cells from 1189 antibody-secreting cells (ASCs) and isolated 94 by CellCellector. We identified a diverse set of heavy chain complementarity-determining region sequences and cloned and expressed 20 into a standard human immunoglobulin G1 antibody format. We further characterized and identified 13 recombinant antibodies that engage soluble and native forms of EGFR. By extrapolating the method to all 400 000 CD138+ B-cells extracted from one EGFR immunized XM, a potential 1196 unique EGFR-specific antibodies could be discovered. CellCelector allows for interrogating the B-cell pool directly and isolating B-cells specific to the therapeutic target of interest. Furthermore, antibody sequences recovered from isolated B-cells engage the native and recombinant target, demonstrating the CellCellector can serve as a platform in antibody discovery.
ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning
Authors: Wei Lesong , Ye Xiucai , Sakurai Tetsuya , Mu Zengchao , Wei Leyi 
Published: January 2022

Abstract

Motivation
Recently, peptides have emerged as a promising class of pharmaceuticals for various diseases treatment poised between traditional small molecule drugs and therapeutic proteins. However, one of the key bottlenecks preventing them from therapeutic peptides is their toxicity toward human cells, and few available algorithms for predicting toxicity are specially designed for short-length peptides.

Results
We present ToxIBTL, a novel deep learning framework by utilizing the information bottleneck principle and transfer learning to predict the toxicity of peptides as well as proteins. Specifically, we use evolutionary information and physicochemical properties of peptide sequences and integrate the information bottleneck principle into a feature representation learning scheme, by which relevant information is retained and the redundant information is minimized in the obtained features. Moreover, transfer learning is introduced to transfer the common knowledge contained in proteins to peptides, which aims to improve the feature representation capability. Extensive experimental results demonstrate that ToxIBTL not only achieves a higher prediction performance than state-of-the-art methods on the peptide dataset, but also has a competitive performance on the protein dataset. Furthermore, a user-friendly online web server is established as the implementation of the proposed ToxIBTL.

Availability and implementation
The proposed ToxIBTL and data can be freely accessible at http://server.wei-group.net/ToxIBTL. Our source code is available at https://github.com/WLYLab/ToxIBTL.

Supplementary information
Supplementary data are available at Bioinformatics online.
scPretrain: multi-task self-supervised learning for cell-type classification
Authors: Zhang Ruiyi , Luo Yunan , Ma Jianzhu , Zhang Ming , Wang Sheng 
Published: January 2022

Abstract

Motivation
Rapidly generated scRNA-seq datasets enable us to understand cellular differences and the function of each individual cell at single-cell resolution. Cell-type classification, which aims at characterizing and labeling groups of cells according to their gene expression, is one of the most important steps for single-cell analysis. To facilitate the manual curation process, supervised learning methods have been used to automatically classify cells. Most of the existing supervised learning approaches only utilize annotated cells in the training step while ignoring the more abundant unannotated cells. In this article, we proposed scPretrain, a multi-task self-supervised learning approach that jointly considers annotated and unannotated cells for cell-type classification. scPretrain consists of a pre-training step and a fine-tuning step. In the pre-training step, scPretrain uses a multi-task learning framework to train a feature extraction encoder based on each dataset’s pseudo-labels, where only unannotated cells are used. In the fine-tuning step, scPretrain fine-tunes this feature extraction encoder using the limited annotated cells in a new dataset.

Results
We evaluated scPretrain on 60 diverse datasets from different technologies, species and organs, and obtained a significant improvement on both cell-type classification and cell clustering. Moreover, the representations obtained by scPretrain in the pre-training step also enhanced the performance of conventional classifiers, such as random forest, logistic regression and support-vector machines. scPretrain is able to effectively utilize the massive amount of unlabeled data and be applied to annotating increasingly generated scRNA-seq datasets.

Availability and implementation
The data and code underlying this article are available in scPretrain: Multi-task self-supervised learning for cell type classification, at https://github.com/ruiyi-zhang/scPretrain and https://zenodo.org/record/5802306.

Supplementary information
Supplementary data are available at Bioinformatics online.
CRAM 3.1: advances in the CRAM file format
Authors: Bonfield James K 
Published: January 2022

Abstract

Motivation
CRAM has established itself as a high compression alternative to the BAM file format for DNA sequencing data. We describe updates to further improve this on modern sequencing instruments.

Results
With Illumina data CRAM 3.1 is 7–15% smaller than the equivalent CRAM 3.0 file, and 50–70% smaller than the corresponding BAM file. Long-read technology shows more modest compression due to the presence of high-entropy signals.

Availability and implementation
The CRAM 3.0 specification is freely available from https://samtools.github.io/hts-specs/CRAMv3.pdf. The CRAM 3.1 improvements are available in a separate OpenSource HTScodecs library from https://github.com/samtools/htscodecs, and have been incorporated into HTSlib.

Supplementary information
Supplementary data are available at Bioinformatics online.
A cystic artery arising from the middle hepatic artery detected during laparoscopic cholecystectomy: a case report
Authors: Kim Sung Hyun , Park Sejin , Choi Jangkyu 
Published: January 2022

Abstract
We herein report a case in which a cystic artery arising from the middle hepatic artery (MHA) was encountered during cholecystectomy. A 42-year-old man visited the outpatient department complaining of chronic epigastric pain and a laparoscopic cholecystectomy was decided upon. During the preoperative evaluation, an interesting finding was observed on computed tomography. The patient had a cystic artery arising from the MHA. An MHA derived from the hilum of the proper hepatic artery runs along the medial border of the gallbladder and enters segment IV. In the operative field, the MHA that entered segment IV was observed. Dissecting downward along the MHA, a cystic artery was observed around the cystic duct. The cystic artery and duct were isolated and each was separately ligated and cut. Rare anatomical variations of the cystic artery, as in this case, can be a pitfall inducing complications during cholecystectomy.
Colocutaneous fistula associated with Crohn’s disease following Kugel patch repair for inguinal hernia: a case report
Authors: Sakai Hiroki , Kubota Koji , Yokoyama Takahide , Shimizu Akira , Notake Tsuyoshi , Masuo Hitoshi , Yoshizawa Takahiro , Hosoda Kiyotaka , Hayashi Hikaru , Yasukawa Koya , Umemura Kentaro , Kamachi Atsushi , Goto Takamune , Tomida Hidenori , Yamazaki Shiori , Soejima Yuji 
Published: January 2022

Abstract
Colocutaneous fistula associated with Crohn’s disease after mesh repair for inguinal hernia has not been previously reported in the literature. We report such case in an 83-year-old man following a preperitoneal repair of a left-sided inguinal hernia using Kugel patch. The patient has Crohn’s disease in remission status for 4 years. One month after inguinal hernia repair, he presented with fever and left-sided inguinal pain and swelling. Computed tomography revealed abscess formation in the preperitoneal and subcutaneous space of the left-sided inguinal region. Colonoscopy showed local exacerbation of Crohn’s disease in the sigmoid colon, and formation of fistula between the sigmoid colon and abdominal wall of the left-sided inguinal region. We performed mesh removal with Hartmann resection following percutaneous abscess drainage. The post-operative course was uneventful, and no sign of recurrence of the hernia was found for 3 years post-operatively.
Two novel species of Arthroderma isolated from domestic cats with dermatophytosis in the United States
Authors: Moskaluk Alex , VandeWoude Sue 
Published: January 2022

Abstract

Dermatophytosis is a superficial fungal infection of keratinized tissues that can occur in humans and other animals. In domestic cats, the majority of cases are caused by Microsporum canis and can spread to other animals and humans via arthrospores. Between 2019 and 2021, 164 cases of suspected dermatophytosis were recorded in animals from a high-volume shelter in California. Samples (hair, nail, and skin scraping) were collected for routine screening from these individuals. One hundred and twenty-six of these were diagnosed as M. canis by culture and internal transcribed spacer (ITS) sequence. In four suspected dermatophytosis cases occurring in kittens in 2019, cultures grown at 20°C yielded fungi with colony morphology more similar to Arthroderma species than Microsporum. Morphologic and microscopic examinations were conducted, and gene segments for the ITS, β-tubulin, and translation elongation factor 1-alpha (TEF1) regions were sequenced from DNA extracted from these cultures. Sequences were aligned to other dermatophytes using maximum likelihood and neighbor-joining trees and were compared to previously described fungal species to assess nucleotide homology. We identified two previously undescribed fungal species, herein proposed as Arthroderma lilyanum sp. nov. and Arthroderma mcgillisianum sp. nov. M. canis co-cultured in two of the four cases. Other physiologic tests supported this diagnosis. These species have significance as potential pathogens and should be considered as rule-outs for dermatophytosis in cats. The potential for infection of other species, including humans, should be considered.

Lay summary
Two novel fungal species were cultured and characterized from four cases of suspected ringworm in cats at an animal shelter in CA, US. These species were genetically distinct from other dermatophytes and are herein described as Arthroderma lilyanum sp. nov. and Arthroderma mcgillisianum sp. nov.
The Pristine survey – XV. A CFHT ESPaDOnS view on the Milky Way halo and disc populations
Authors: Lucchesi R , Lardo C , Jablonka P , Sestito F , Mashonkina L , Arentsen A , Suter W , Venn K , Martin N , Starkenburg E , Aguado D , Hill V , Kordopatis G , Navarro J F , González Hernández J I , Malhan K , Yuan Z 
Published: January 2022

ABSTRACT
We present a one-dimensional, local thermodynamic equilibrium homogeneous analysis of 132 stars observed at high resolution with ESPaDOnS. This represents the largest sample observed at high resolution (R ∼ 40 000) from the Pristine survey. This sample is based on the first version of the Pristine catalogue and covers the full range of metallicities from [Fe/H] ∼−3 to ∼+0.25, with nearly half of our sample (58 stars) composed of very metal-poor (VMP) stars ([Fe/H] ≤ −2). This wide range of metallicities provides the opportunity of a new detailed study of the Milky Way stellar population. Because it includes both dwarf and giant stars, it also enables the analysis of any potential bias induced by the Pristine selection process. Based on Gaia EDR3, the orbital analysis of this Pristine-ESPaDOnS sample shows that it is composed of 65 halo stars and 67 disc stars. After a general assessment of the sample chemical properties with the α-elements Mg and Ca, we focus on the abundance of carbon and the neutron capture elements Ba and Sr. While most of our VMP subsample is carbon normal, we also find that 14 stars out of the 38 stars with [Fe/H] ≤ −2 and measured carbon abundances turn out to be carbon-enhanced metal-poor (CEMP) stars. We show that these CEMP stars are nearly exclusively (i.e. 12 stars out of 14) in the regime of low luminosity, unevolved, dwarf stars, which we interpret as the consequence of bias of the Pristine filter against C-rich giants. Among the VMP stars, we identify two CEMP stars with no enhancement in neutron-capture process elements and another one enriched in s-process element. Finally, one VMP star is found with a very low [Sr/Fe] abundance ratio for its metallicity, as expected if it had been accreted from an ultra-faint dwarf galaxy.
LRG-BEASTS: Sodium absorption and Rayleigh scattering in the atmosphere of WASP-94A b using NTT/EFOSC2
Authors: Ahrer E , Wheatley P J , Kirk J , Gandhi S , King G W , Louden T 
Published: January 2022

ABSTRACT
We present an optical transmission spectrum for WASP-94A b, the first atmospheric characterization of this highly-inflated hot Jupiter. The planet has a reported radius of $1.72^{+0.06}_{-0.05}$ RJup, a mass of only $0.456^{+0.032}_{-0.036}$ MJup, and an equilibrium temperature of 1508 ± 75 K. We observed the planet transit spectroscopically with the EFOSC2 instrument on the ESO New Technology Telescope (NTT) at La Silla, Chile: the first use of NTT/EFOSC2 for transmission spectroscopy. We achieved an average transit-depth precision of 128 ppm for bin widths of ∼200 Å. This high precision was achieved in part by linking Gaussian Process hyperparameters across all wavelength bins. The resulting transmission spectrum, spanning a wavelength range of 3800–7140 Å, exhibits a sodium absorption with a significance of 4.9σ, suggesting a relatively cloud-free atmosphere. The sodium signal may be broadened, with a best-fitting width of $78_{-32}^{+67}$ Å in contrast to the instrumental resolution of 27.2 ± 0.2 Å. We also detect a steep slope in the blue end of the transmission spectrum, indicating the presence of Rayleigh scattering in the atmosphere of WASP-94A b. Retrieval models show evidence for the observed slope to be super-Rayleigh and potential causes are discussed. Finally, we find narrow absorption cores in the CaII H&K lines of WASP-94A, suggesting the star is enshrouded in gas escaping the hot Jupiter.
Clump survival and migration in VDI galaxies: an analytical model versus simulations and observations
Authors: Dekel Avishai , Mandelker Nir , Bournaud Frederic , Ceverino Daniel , Guo Yicheng , Primack Joel 
Published: January 2022

ABSTRACT
We address the nature of the giant clumps in high-z galaxies that undergo violent disc instability, distinguishing between long-lived and short-lived clumps. We study the evolution of long-lived clumps during migration through the disc via an analytical model tested by simulations and confront theory with CANDELS-HST observations. The clump ‘bathtub’ model, which considers gas and stellar gain and loss, involves four parameters: the accretion efficiency α, the star formation rate (SFR) efficiency ϵd, and the outflow mass-loading factors for gas and stars, η and ηs. The corresponding time-scales are comparable to the migration time, two-three orbital times. The accretion-rate dependence on clump mass, gas, and stars, allows an analytical solution involving exponential growing and decaying modes. For the fiducial parameter values there is a main evolution phase where the SFR and gas mass are constant and the stellar mass is rising linearly with time. This makes the inverse specific SFR an observable proxy for clump age. When η or ϵd are high, or α is low, the decaying mode induces a decline of SFR and gas mass till the migration ends. Later, the masses and SFR approach an hypothetical exponential growth with a constant specific SFR. The model matches simulations with different, moderate feedbacks, both in isolated and cosmological settings. The observed clumps agree with our predictions, indicating that the massive clumps are long-lived and migrating. A challenge is to model feedback that is non-disruptive in massive clumps but suppresses SFR to match the galactic stellar-to-halo mass ratio.