bluuebunny/crossref_metadata_2025_split huggingface dataset:
KmerKeys: a web resource for searching indexed genome assemblies and variants
Authors: Pavlichin Dmitri S , Lee HoJoon , Greer Stephanie U , Grimes Susan M , Weissman Tsachy , Ji Hanlee P 
Published: April 2022

AbstractK-mers are short DNA sequences that are used for genome sequence analysis. Applications that use k-mers include genome assembly and alignment. However, the wider bioinformatic use of these short sequences has challenges related to the massive scale of genomic sequence data. A single human genome assembly has billions of k-mers. As a result, the computational requirements for analyzing k-mer information is enormous, particularly when involving complete genome assemblies. To address these issues, we developed a new indexing data structure based on a hash table tuned for the lookup of short sequence keys. This web application, referred to as KmerKeys, provides performant, rapid query speeds for cloud computation on genome assemblies. We enable fuzzy as well as exact sequence searches of assemblies. To enable robust and speedy performance, the website implements cache-friendly hash tables, memory mapping and massive parallel processing. Our method employs a scalable and efficient data structure that can be used to jointly index and search a large collection of human genome assembly information. One can include variant databases and their associated metadata such as the gnomAD population variant catalogue. This feature enables the incorporation of future genomic information into sequencing analysis. KmerKeys is freely accessible at https://kmerkeys.dgi-stanford.org.
Cell type identification in spatial transcriptomics data can be improved by leveraging cell-type-informative paired tissue images using a Bayesian probabilistic model
Authors: Zubair Asif , Chapple Richard H , Natarajan Sivaraman , Wright William C , Pan Min , Lee Hyeong-Min , Tillman Heather , Easton John , Geeleher Paul 
Published: April 2022

Abstract
Spatial transcriptomics technologies have recently emerged as a powerful tool for measuring spatially resolved gene expression directly in tissues sections, revealing cell types and their dysfunction in unprecedented detail. However, spatial transcriptomics technologies are limited in their ability to separate transcriptionally similar cell types and can suffer further difficulties identifying cell types in slide regions where transcript capture is low. Here, we describe a conceptually novel methodology that can computationally integrate spatial transcriptomics data with cell-type-informative paired tissue images, obtained from, for example, the reverse side of the same tissue section, to improve inferences of tissue cell type composition in spatial transcriptomics data. The underlying statistical approach is generalizable to any spatial transcriptomics protocol where informative paired tissue images can be obtained. We demonstrate a use case leveraging cell-type-specific immunofluorescence markers obtained on mouse brain tissue sections and a use case for leveraging the output of AI annotated H&E tissue images, which we used to markedly improve the identification of clinically relevant immune cell infiltration in breast cancer tissue. Thus, combining spatial transcriptomics data with paired tissue images has the potential to improve the identification of cell types and hence to improve the applications of spatial transcriptomics that rely on accurate cell type identification.
VRprofile2: detection of antibiotic resistance-associated mobilome in bacterial pathogens
Authors: Wang Meng , Goh Ying-Xian , Tai Cui , Wang Hui , Deng Zixin , Ou Hong-Yu 
Published: April 2022

Abstract
VRprofile2 is an updated pipeline that rapidly identifies diverse mobile genetic elements in bacterial genome sequences. Compared with the previous version, three major improvements were made. First, the user-friendly visualization could aid users in investigating the antibiotic resistance gene cassettes in conjunction with various mobile elements in the multiple resistance region with mosaic structure. VRprofile2 could compare the predicted mobile elements to the collected known mobile elements with similar architecture. A new mobilome indicator was proposed to give an overall estimation of the mobilome size in individual bacterial genomes. Second, the relationship between antibiotic resistance genes, mobile elements, and host strains would be efficiently examined with the aid of predicted strain's sequence typing, the incompatibility group and the transferability of plasmids. Finally, the updated back-end database, MobilomeDB2, now collected nearly a thousand active mobile elements retrieved from literature or based on prediction. The pre-computed results of the antibiotic resistance gene-carrying mobile elements of &gt;5500 ESKAPEE genomes were also provided. We expect that VRprofile2 will provide better support for researchers interested in bacterial mobile elements and the dissemination of antibiotic resistance. VRprofile2 is freely available to all users without any login requirement at https://tool2-mml.sjtu.edu.cn/VRprofile.
Intraspecific de novo gene birth revealed by presence–absence variant genes in Caenorhabditis elegans
Authors: Lee Bo Yun , Kim Jun , Lee Junho 
Published: April 2022

Abstract
Genes embed their evolutionary history in the form of various alleles. Presence–absence variants (PAVs) are extreme cases of such alleles, where a gene present in one haplotype does not exist in another. Because PAVs may result from either birth or death of a gene, PAV genes and their alternative alleles, if available, can represent a basis for rapid intraspecific gene evolution. Using long-read sequencing technologies, this study traced the possible evolution of PAV genes in the PD1074 and CB4856 C. elegans strains as well as their alternative alleles in 14 other wild strains. We updated the CB4856 genome by filling 18 gaps and identified 46 genes and 7,460 isoforms from both strains not annotated previously. We verified 328 PAV genes, out of which 46 were C. elegans-specific. Among these possible newly born genes, 12 had alternative alleles in other wild strains; in particular, the alternative alleles of three genes showed signatures of active transposons. Alternative alleles of three other genes showed another type of signature reflected in accumulation of small insertions or deletions. Research on gene evolution using both species-specific PAV genes and their alternative alleles may provide new insights into the process of gene evolution.
Clinical Characteristics, Health Care Utilization, and Outcomes Among Patients in a Pilot Surveillance System for Invasive Mold Disease—Georgia, United States, 2017–2019
Authors: Gold Jeremy A W , Revis Andrew , Thomas Stepy , Perry Lewis , Blakney Rebekah A , Chambers Taylor , Bentz Meghan L , Berkow Elizabeth L , Lockhart Shawn R , Lysen Colleen , Nunnally Natalie S , Jordan Alexander , Kelly Hilary C , Montero Alejandro J , Farley Monica M , Oliver Nora T , Pouch Stephanie M , Webster Andrew S , Jackson Brendan R , Beer Karlyn D 
Published: April 2022

Abstract

Background
Invasive mold diseases (IMDs) cause severe illness, but public health surveillance data are lacking. We describe data collected from a laboratory-based, pilot IMD surveillance system.

Methods
During 2017–2019, the Emerging Infections Program conducted active IMD surveillance at 3 Atlanta-area hospitals. We ascertained potential cases by reviewing histopathology, culture, and Aspergillus galactomannan results and classified patients as having an IMD case (based on European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group [MSG] criteria) or a non-MSG IMD case (based on the treating clinician’s diagnosis and use of mold-active antifungal therapy). We described patient features and compared patients with MSG vs non-MSG IMD cases.

Results
Among 304 patients with potential IMD, 104 (34.2%) met an IMD case definition (41 MSG, 63 non-MSG). The most common IMD types were invasive aspergillosis (n = 66 [63.5%]), mucormycosis (n = 8 [7.7%]), and fusariosis (n = 4 [3.8%]); the most frequently affected body sites were pulmonary (n = 66 [63.5%]), otorhinolaryngologic (n = 17 [16.3%]), and cutaneous/deep tissue (n = 9 [8.7%]). Forty-five (43.3%) IMD patients received intensive care unit–level care, and 90-day all-cause mortality was 32.7%; these outcomes did not differ significantly between MSG and non-MSG IMD patients.

Conclusions
IMD patients had high mortality rates and a variety of clinical presentations. Comprehensive IMD surveillance is needed to assess emerging trends, and strict application of MSG criteria for surveillance might exclude over one-half of clinically significant IMD cases.
Osteoradionecrosis of the craniotomy flap: a rare complication of stereotactic radiosurgery
Authors: Schlafstein Ashley , Shu Hui-Kuo 
Published: April 2022

Abstract
Osteoradionecrosis (ORN), ischemic necrosis of irradiated bone without evidence of persisting or recurrent tumor, is a known complication of radiation therapy. ORN of the skull has not been reported following stereotactic radiosurgery (SRS). We report two cases of ORN of the skull following SRS for recurrent meningiomas post-resection. Both patients developed ORN in their craniotomy flaps in areas that received high doses of radiation due to their proximity to the recurrent tumors. In each case, the ORN was asymptomatic and was detected on surveillance magnetic resonance imaging. Both patients were followed closely with imaging that ultimately revealed either stability or improvement in the ORN, confirming the diagnosis without the need for biopsy. The cases reveal a role for close imaging surveillance instead of immediate biopsy in patients with new enhancement involving bone in high-dose radiation treatment regions.
Strong site-specific association of pharyngeal cultures with the onset of psoriatic arthritis and psoriasis, regardless of pathogen
Authors: Thrastardottir Telma , Meer Elana , Hauksdottir Arna , Gudbjornsson Bjorn , Kristinsson Sigurdur Yngvi , Ogdie Alexis , Love Thorvardur Jon 
Published: April 2022

Abstract

Objectives
The objective of this study was to evaluate any association between culture site / culture result / pathogen and incident PsA or psoriasis.

Methods
Records of all samples sent for culture from a large population during a 3-year period were linked with nationwide registry data on diagnoses and death over a 15-year period. The main outcomes of interest were incident diagnoses of PsA and psoriasis, defined by International Classification of Diseases (ICD) codes. The effect of culture site, culture result (positive vs negative), and pathogen (Streptococcus vs negative culture) on the risk of developing PsA and psoriasis was calculated using Cox proportional hazards models adjusted for age and gender.

Results
A total of 313 235 bacterial cultures from 128 982 individuals were analysed. Comparing individuals with pharyngeal cultures to those with urine cultures, the hazard ratio for incident PsA was 8.78 [95% confidence interval (CI) 3.23, 23.91] and for incident psoriasis it was 8.00 (95% CI 5.28, 12.12). Most of the risk was concentrated in the first 50 days after the culture date. Increased risk was also found when comparing individuals with cultures from the pharynx with those with cultures from the nasopharynx and blood. An association with streptococci was not found, neither in the pharynx nor at any other site. A positive bacterial culture from any site was associated with reduced risk for both PsA and psoriasis.

Conclusion
There is a strong site-specific association between pharyngeal culture samples and an increased risk of PsA and psoriasis, regardless of the pathogen. This may indicate that the site of infection, rather than the pathogen, is associated with increased risk.
A number of legal principles have been reaffirmed in relation to section 47 applications arising from In The Matter The XYZ Trusts
Authors: Bernard Stephanie 
Published: April 2022

Abstract
In The Matter The XYZ Trusts is an important case because it confirmed a number of very useful legal principles. In relation to applications pursuant to section 47 of the Bermuda Trustee Act 1975, it confirmed that such applications may be used in series for the blessing of various stages of a large transaction, the test to be used when asking for the blessing of a momentous decision and that in relation to the variation of a trust it will not create a new settlement. Finally, it confirmed the Bermuda Court’s willingness to issue confidentiality orders in cases involving the administration of private trusts.
Three new clades of putative viral RNA-dependent RNA polymerases with rare or unique catalytic triads discovered in libraries of ORFans from powdery mildews and the yeast of oenological interest Starmerella bacillaris
Authors: Forgia Marco , Chiapello M , Daghino Stefania , Pacifico D , Crucitti D , Oliva D , Ayllon M , Turina M , Turina M 
Published: April 2022

Abstract
High throughput sequencing allowed the discovery of many new viruses and viral organizations increasing our comprehension of virus origin and evolution. Most RNA viruses are currently characterized through similarity searches of annotated virus databases. This approach limits the possibility to detect completely new virus-encoded proteins with no detectable similarities to existing ones, i.e. ORFan proteins. A strong indication of the ORFan viral origin in a metatranscriptome is the lack of DNA corresponding to an assembled RNA sequence in the biological sample. Furthermore, sequence homology among ORFans and evidence of co-occurrence of these ORFans in specific host individuals provides further indication of a viral origin. Here, we use this theoretical framework to report the finding of three conserved clades of protein-coding RNA segments without a corresponding DNA in fungi. Protein sequence and structural alignment suggest these proteins are distantly related to viral RNA-dependent RNA polymerases (RdRP). In these new putative viral RdRP clades, no GDD catalytic triad is present, but the most common putative catalytic triad is NDD and a clade with GDQ, a triad previously unreported at that site. SDD, HDD, and ADD are also represented. For most members of these three clades, we were able to associate a second genomic segment, coding for a protein of unknown function. We provisionally named this new group of viruses ormycovirus. Interestingly, all the members of one of these sub-clades (gammaormycovirus) accumulate more minus sense RNA than plus sense RNA during infection.
Persistent But Not Transient Acute Kidney Injury Was Associated With Lower Transplant-Free Survival in Patients With Acute Liver Failure: A Multicenter Cohort Study*
Authors: Cardoso Filipe S. , Fidalgo Pedro , Bagshaw Sean M. , Gottfried Michelle , Tujios Shannan , Olson Jody C. , Lee William M. , Karvellas Constantine J. ,   for the U.S. Acute Liver Failure Study Group
Published: April 2022

OBJECTIVES:
Acute liver failure (ALF) is an orphan disease often complicated by acute kidney injury (AKI). We assessed the impact of transient versus persistent AKI on survival in patients with ALF.

DESIGN:
International multicenter retrospective cohort.

SETTING:
U.S. ALF Study Group prospective registry.

PATIENTS:
Patients with greater than or equal to 18 years and ALF in the registry from 1998 to 2016 were included. Patients with less than 3 days of follow-up, without kidney function evaluation on day 3, or with cirrhosis were excluded.

INTERVENTIONS:
AKI was defined by Kidney Disease Improving Global Outcomes guidelines on day 1. Kidney recovery was defined on day 3 as transient AKI, by a return to no-AKI within 48 hours or persistent AKI if no such recovery or renal replacement therapy (RRT) was observed. Primary outcome was transplant-free survival (TFS) at 21 days.

MEASUREMENTS AND MAIN RESULTS:
Among 1,071 patients with ALF, 339 (31.7%) were males, and median (interquartile range) age was 39 years (29–51 yr). Acetaminophen-related ALF was found in 497 patients (46.4%). On day 1, 485 of 1,071 patients (45.3%) had grade 3–4 hepatic encephalopathy (HE), 500 of 1,070 (46.7%) required invasive mechanical ventilation (IMV), 197 of 1,070 (18.4%) were on vasopressors, and 221 of 1,071 (20.6%) received RRT. On day 1, 673 of 1,071 patients (62.8%) had AKI. On day 3, 72 of 1,071 patients (6.7%) had transient AKI, 601 of 1,071 (56.1%) had persistent AKI, 71 of 1,071 (6.6%) had late onset AKI, and 327 of 1,071 (30.5%) remained without AKI. Following adjustment for confounders (age, sex, race, etiology, HE grade, use of IMV and vasopressors, international normalized ratio, and year), although persistent acute kidney injury (adjusted odds ratio [aOR] [95% CI] 0.62 [0.44–0.88]) or late onset AKI (aOR [95% CI] 0.48 [0.26–0.89]) was associated with lower TFS, transient AKI was not (aOR [95% CI] 1.89 [0.99–3.64]).

CONCLUSIONS:
In a multicenter cohort of patients with ALF, persistent but not transient AKI was independently associated with lower short-term TFS.
Toxoplasma gondii Infection and Aggression in Autistic Children
Authors: Hamid Najmeh , Azizy Boshra , Hamidinejad Hossein 
Published: April 2022

Background:

Toxoplasmosis is an infectious disease caused by the obligatory intracellular parasite Toxoplasma gondii. The main aim of this study was to evaluate a possible relationship between aggression in autistic children with infection by T. gondii.

Methods:
The research design was an analytical (comparative) cross sectional study. The participants included (N = 100) subjects (50 autistic and 50 normal children) between 3 and 12 years old. They were matched for age, socioeconomic status, lack of physical and mental illness. The instruments were preschool aggression scale and enzyme-linked immunosorbent assay procedure to essay the blood sample test. Five milliliters of blood samples were collected to assess the presence of T. gondii infection.

Results:
The results showed that autistic children had a higher rate of infection by T. gondii than normal children. Furthermore, children infected with T. gondii were more aggressive than the noninfected group.

Conclusions:
In autistic children, T. gondii infection was significantly higher than in the normal group. Also, autistic children who were infected with the parasite were more aggressive.
Subsartorius Fascial Plane Hydrodissection as Novel Treatment for Hunter's Canal Syndrome
Authors: Eliot Hu Yao-Wen , Ridings Catherine 
Published: April 2022

Abstract:
Saphenous entrapment neuropathy in the distal thigh most commonly occurs at Hunter's canal and is characterized by neurologic symptoms distal to the midthigh in the saphenous nerve distribution. Presented is a 23-year-old active duty female service member with left medial knee pain worse with knee flexion and extension. Evaluation raised suspicion for saphenous nerve entrapment at Hunter's canal, and ultrasound-guided subsartorius fascial plane hydrodissection was performed in addition to focused rehabilitation of the adductor and core musculature. No reports of this treatment have been published to date. This case introduces ultrasound-guided subsartorius fascial plane hydrodissection as novel treatment in Hunter's canal syndrome.
Incremental Effects of Subsequent Concussions on Cognitive Symptoms in the Sport Concussion Assessment Tool
Authors: Chen Jian , Oddson Bruce , Skrinar Hannah 
Published: April 2022

Objective:
Patients who are fully recovered from a concussion may still be more vulnerable in the face of subsequent concussions. This study examines symptoms associated with repeated concussions in young and otherwise healthy adults.

Design:
Cross sectional.

Setting:
Institutional study at a university setting.

Participants:
University students with a history of concussion.

Independent Variables:
Participants were grouped based on numbers of concussions.

Main Outcome Measures:
The impact of incremental concussion on symptom clusters in Sport Concussion Assessment Tools 5 and Spearman ranking correlation coefficients between symptom clusters.

Results:
One hundred thirty-five participants reported having had 1 concussion, 63 reported 2 concussions, 50 reported 3 concussions, and 43 reported 4 to 6 concussions. Total severity scores over the range of concussion number (1, 2, 3, and greater than 3) did not show a clear incremental effect. However, average scores of cognitive symptoms rose with each subsequent concussion (P ≤ 0.05). The largest incremental effect observed was that of second concussions on emotional symptom scores (t = 5.85, P < 0.01). Symptoms in the emotional and cognitive clusters were the most correlated regardless of the number of reported concussions; the correlations were lowest with symptoms associated with sensitivity to light or noise.

Conclusions:
The incremental rise of cognitive symptom scores with each concussion affirms the importance of cognitive impairment in concussion assessment and implies a cumulative brain vulnerability that persists even after symptom resolution. The cognitive-emotional symptom clusters may reflect underlying concussion-induced impairments in the corticostriatothalamocortical (CSTC) networks, although sensitivity symptoms are potentially attributable to different neural correlates.
Outcome and Determinants of Neutropenic Enterocolitis in Pediatric Cancer Patients
Authors: Sahoo Debasish , Seth Rachna , Chaudhry Rama , Naranje Priyanka , Ahuja Vineet , Dwivedi Sada N. , Gupta Aditya K. , Meena Jagdish P. 
Published: April 2022

Background:
Neutropenic enterocolitis (NEC) is a dreaded complication of chemotherapy. There is scant literature regarding incidence, clinical features, and determinants. The understanding of gut dysbiosis in NEC and pediatric cancer is evolving.

Methods:
Pediatric cancer patients with neutropenia and gastrointestinal symptoms were evaluated for NEC with contrast-enhanced computed tomography abdomen. Clinical, imaging, and laboratory features were analyzed. Fecal samples were analyzed for fecal calprotectin by sandwich enzyme-linked immunoassay and gut microbiota by conventional culture and compared with healthy controls and children without NEC.

Results:
NEC was diagnosed in 44 children based on clinical and imaging features with incidence of 7.4% (4 had recurrent episodes). Common manifestations included fever (98%), pain abdomen (88%), and diarrhea (83%). Hypoalbuminemia was observed in 78% of patients. Large bowel involvement (94%) with diffuse bowel involvement (63%) and pancolitis (64%) were common. Fecal calprotectin was significantly elevated in NEC group than non-NEC group and healthy controls (median: 87, 53, and 42 µg/g, respectively). A higher degree of gut dysbiosis was observed in children with NEC with higher isolation of Bacteroides and infrequent isolation of Lactobacilli. Mortality rate of 23% was observed. Only the presence of free fluid predicted higher mortality. Though levels of fecal calprotectin and gut dysbiosis were higher in NEC, they did not increase mortality. Isolation of Bacteroides and absence of Lactobacilli predicted a longer duration of intravenous alimentation.

Conclusions:
NEC caused significant morbidity and mortality in pediatric cancer patients. Gut dysbiosis was significantly higher in NEC group suggesting a role in pathogenesis and influencing outcome. This highlights the role of targeted interventions towards gut dysbiosis like prebiotics and probiotics.