bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patient Demographics and the Utilization of a Novel 3-Anatomic-Site Testing Panel Including Rectal Self-Collection as Compared With Usual Care Testing
Authors: Horberg Michael , Eberhart Lindsay , Bhatia Mamta , Jonas Cabell , Cherico-Hsii Sara , Tamrat Yonas , Bhandari Binamrata , Kadlecik Peter , Gahunia Mona K. 
Published: November 2021

Background
At Kaiser Permanente Mid-Atlantic States, we designed a 3-anatomic-site panel (urine, oropharynx, and rectum) with a self-collect feature for rectal sites. We compared the proportion tested at each anatomic site, demographic factors, and HIV status between those who received the 3-site panel versus usual care.

Methods
Patients entered our laboratories without a prior appointment and underwent urine (usual care [patient collected]), oropharynx (laboratory technician collected), and rectal site (patient collected) testing. Providers recommended the panel to their patients. Patients then had the choice to accept or to reject the panel. Multivariate and logistic regressions were conducted to explore the relationship of age, sex, race, and HIV status with Neisseria gonorrhoeae (GC) and Chlamydia trachomatis (CT) test results as well as the type of testing (3-site panel vs. usual care testing) received.

Results
A total of 145,854 patients received usual care testing as compared with 9227 who received the panel. For those who underwent usual care testing, 4.0% tested positive for CT and 0.85% for GC. For those who received the panel, 9.1% tested positive for CT and 6.4% for GC. Those who received the 3-site panel were more likely to test positive for CT (odds ratio [OR], 2.70; confidence interval [CI], 2.46–2.97) and GC (OR, 4.00; CI, 3.59–4.64). White patients were the most likely to receive the panel compared with Black patients (OR, 3.14; CI, 2.96–3.33). Patients with HIV had greater odds of undergoing the panel (OR, 15.62; CI, 14.67–16.64) and of testing positive for CT (OR, 1.27; CI, 1.07–1.51) and GC (OR, 1.39; CI, 1.14–1.68).

Conclusions
Patients who received the panel had higher odds of testing positive for CT and GC compared with patients with usual testing. Physician training may address the racial and sex differences observed in the panel enrollment and increase utilization. Self-collection for rectal sites should lead to higher detection of CT and GC.
Clinical Integration of a Highly Accurate Polymerase Chain Reaction Point-of-Care Test Can Inform Immediate Treatment Decisions for Chlamydia, Gonorrhea, and Trichomonas
Authors: Dawkins Megan , Bishop Lisa , Walker Paula , Otmaskin Danielle , Ying Julia , Schmidt Ryan , Harnett Glenn , Abraham Teresa , Gaydos Charlotte A. , Schoolnik Gary , DiBenedetto Kevin 
Published: November 2021

Background
Accurate same-day sexually transmitted infection (STI) diagnostic testing is generally unavailable, leading to syndromic management with high rates of overtreatment and undertreatment. We analyzed the ease of integration of the Visby STI Panel into clinical practice, studied acceptance by patients and clinic personnel, and assessed the potential to inform accurate treatment decisions.

Methods
In a cross-sectional single-visit study of 55 women aged 18 to 56 years, women self-collected vaginal swab samples that were analyzed using the Visby STI Panel for Chlamydia trachomatis, Neisseria gonorrhoeae (NG), and Trichomonas vaginalis (TV). Results were compared with standard-of-care clinic results from send-out laboratory polymerase chain reaction tests. Surveys assessed patient and device operator experiences with the Visby STI Panel and clinicians' perceived need for and acceptance of the device. Time parameters were measured to evaluate the impact on clinical workflow, and syndromic treatment decisions were compared with anticipated treatment based on the Visby STI Panel results.

Results
Patients strongly agreed that sample self-collection was easy, and operators reported the device easy to use. Clinicians valued the rapid return of results, and patients were comfortable waiting up to 30 minutes to receive them. In 13 of 15 cases, the Visby STI Panel correctly identified undertreated patients as infected and correctly identified all 33 incidences of overtreatment.

Conclusions
Clinical adoption of the Visby STI Panel into primary care clinics and doctors' offices could reduce overtreatment and undertreatment of STIs. If integrated efficiently into the clinical workflow, the test would have minimal impact on staff time and visit duration for patients.
The Most Current Algorithms for the Treatment and Prevention of Hypertrophic Scars and Keloids: A 2020 Update of the Algorithms Published 10 Years Ago
Authors: Ogawa Rei 
Published: November 2021

Background:
In 2010, this Journal published my comprehensive review of the literature on hypertrophic scars and keloids. In that article, I presented evidence-based algorithms for the prevention and treatment of these refractory pathologic scars. In the ensuing decade, substantial progress has been made in the field, including many new randomized controlled trials. To reflect this, I have updated my review.

Methods:
All studies were evaluated for methodologic quality. Baseline characteristics of patients were extracted along with the interventions and their outcomes. Systematic reviews, meta-analyses, and comprehensive reviews were included if available.

Results:
Risk factors that promote hypertrophic scar and keloid growth include local factors (tension on the wound/scar), systemic factors (e.g., hypertension), genetic factors (e.g., single-nucleotide polymorphisms), and lifestyle factors. Treatment of hypertrophic scars depends on scar contracture severity: if severe, surgery is the first choice. If not, conservative therapies are indicated. Keloid treatment depends on whether they are small and single or large and multiple. Small and single keloids can be treated radically by surgery with adjuvant therapy (e.g., radiotherapy) or multimodal conservative therapy. For large and multiple keloids, volume- and number-reducing surgery is a choice. Regardless of the treatment(s), patients should be followed up over the long term. Conservative therapies, including gel sheets, tape fixation, topical and injected external agents, oral agents, and makeup therapy, should be administered on a case-by-case basis.

Conclusions:
Randomized controlled trials on pathologic scar management have increased markedly over the past decade. Although these studies suffer from various limitations, they have greatly improved hypertrophic scar and keloid management. Future high-quality trials are likely to improve the current hypertrophic scar and keloid treatment algorithms further.
Factors related to indoor prosthetic use in individuals with unilateral lower limb amputation
Authors: Tezuka Yusuke , Chin Takaaki , Azuma Yuji , Miura Yasushi 
Published: November 2021

Background:
The rate of indoor prosthetic use in people with lower limb amputation (LLA) is lower than that of outdoor use. Very few studies of indoor prosthetic use have been conducted, and no studies have focused on the perspective of instrumental activities of daily living (IADLs).

Objectives:
To assess the indoor prosthetic use of individuals with unilateral LLA from the perspective of IADLs.

Study design:
Cross-sectional study.

Methods:
A total of 162 people with LLA participated in this study. Based on the information obtained from a questionnaire and medical records, the relationships between each outcome and indoor prosthetic use were assessed by univariate analysis and multivariate logistic regression analysis.

Results:
Of the 110 respondents (72.8%), 6 participants did not use the prosthesis or used it for cosmesis. With respect to the prosthetic users (n = 104), 74 (71.2%) used their prosthesis indoors and outdoors and 30 (28.8%) used it only outdoors, but none used it indoors only. On univariate analysis, five items were identified: household size, amputation level, domestic chores and outdoor activities of the Frenchay Activities Index, and difficulty donning/doffing the prosthesis. Small household, transtibial amputation, and a high score on the domestic chores of the Frenchay Activities Index (cutoff value 9.0 points) were independently associated with indoor prosthetic use.

Conclusions:
Training of motions that are desirable to use the prosthesis and participation in domestic chores frequently based on IADLs before hospitalization may increase the frequency of prosthesis use in people with transfemoral amputation who use their prosthesis outdoors.
Development and Preliminary Validation of a Virtual Reality Approach for Measurement of Torsional Strabismus
Authors: Bindiganavale Megha , Buickians David , Lambert Scott R. , Bodnar Zachary M. , Moss Heather E. 
Published: November 2021

Background:
Double Maddox rod (DMR), the gold-standard method for in-office measurement of cyclodeviation, requires an examiner and specialized equipment. The objective of this study was to develop a virtual reality (VR) technique for measurement of cyclodeviation and validate this against the DMR.

Methods:
A VR-DMR was implemented using a smartphone and commercially available VR viewer. The app displayed a line to each eye and accepted touch inputs from the user to rotate the lines into perceived alignment. VR-DMR cyclodeviation measurements were compared with traditional DMR (T-DMR) cyclodeviation measurements in adults with and without strabismus and children without strabismus.

Results:
Thirty-one subjects were studied (age 5–88 years, 20 with strabismus). VR-DMR had similar test–retest reliability as T-DMR. VR-DMR was highly correlated with T-DMR (r2 = 0.94, linear regression slope 1.12) with a slight positive bias (linear regression y intercept 1°). VR-DMR was preferred by 54% of subjects with 29% having no preference.

Conclusions:
A VR method of ocular cyclodeviation measurement using sensory techniques was implemented using commercially available hardware. VR measurements compared favorably with gold-standard DMR measurements, and user feedback was positive. The VR methodology has application for in office and home use by nonexperts for purposes of strabismus monitoring.
Isolation and characterisation of quercitrin as a potent anti-sickle cell anaemia agent from Alchornea cordifolia
Authors: Adeniyi Olayemi , Baptista Rafael , Bhowmick Sumana , Cookson Alan , Nash Robert , Winters Ana , Mur Luis A. J. 
Published: November 2021

AbstractAlchornea cordifolia Müll. Arg. (commonly known as Christmas Bush) has been used traditionally in Africa to treat sickle cell anaemia (a recessive disease, arising from the S haemoglobin [Hb] allele) but the active compounds are yet to be characterised. Herein we describe the use of sequential fractionation coupled with in vitro anti-sickling assays to purify the active component. Sickling was induced in HbSS genotype blood samples using sodium metabisulphite (Na2S2O5) or incubation in 100 % N2. Methanol extracts of A. cordifolia leaves and its sub-fractions showed >70 % suppression of HbSS erythrocyte sickling. Purified compound demonstrated 87.2 ± 2.39 % significant anti-sickling activity and 93.1 ± 2.69 % erythrocyte sickling-inhibition at 0.4 mg/mL. Nuclear magnetic resonance (NMR) spectra and high-resolution mass spectroscopy identified it as quercitrin (quercetin 3-rhamnoside). Purified quercitrin also inhibited the polymerisation of isolated HbS and stabilized sickle erythrocytes membranes. Metabolomic comparisons of blood samples using flow-infusion electrospray-high resolution mass spectrometry indicated that quercitrin could convert HbSS erythrocyte metabolomes to be similar to HbAA. Sickling was associated with changes in anti-oxidants, anaerobic bioenergy and arachidonic acid metabolism, all of which were reversed by quercitrin. The findings described could inform efforts directed to the development of an anti-sickling drug or quality control assessments of A. cordifolia preparations.
Jointly Optimized Spatial Histogram UNET Architecture (JOSHUA) for Adipose Tissue Segmentation
Authors: Peeples Joshua K. , Jameson Julie F. , Kotta Nisha M. , Grasman Jonathan M. , Stoppel Whitney L. , Zare Alina 
Published: November 2021

AbstractObjectiveWe quantify adipose tissue deposition at surgical sites as a function of biomaterial implantation.Impact StatementTo our knowledge, this study is the first investigation to apply convolutional neural network (CNN) models to identify and segment adipose tissue in histological images from silk fibroin biomaterial implants.IntroductionWhen designing biomaterials for the treatment of various soft tissue injuries and diseases, one must consider the extent of adipose tissue deposition. In this work, we implant silk fibroin biomaterials in a rodent subcutaneous injury model. Current strategies for quantifying adipose tissue after biomaterial implantation are often tedious and prone to human bias during analysis.MethodsWe used CNN models with novel spatial histogram layer(s) that can more accurately identify and segment regions of adipose tissue in hematoxylin and eosin (H&E) and Masson’s Trichrome stained images, allowing for determination of the optimal biomaterial formulation. We compared the method, Jointly Optimized Spatial Histogram UNET Architecture (JOSHUA), to the baseline UNET model and an extension of the baseline model, Attention UNET, as well as to versions of the models with a supplemental “attention”-inspired mechanism (JOSHUA+ and UNET+).ResultsThe inclusion of histogram layer(s) in our models shows improved performance through qualitative and quantitative evaluation.ConclusionOur results demonstrate that the proposed methods, JOSHUA and JOSHUA+, are highly beneficial for adipose tissue identification and localization. The new histological dataset and code for our experiments are publicly available.
All-optical electrophysiology with improved genetically encoded voltage indicators reveals interneuron network dynamics in vivo
Authors: Tian He , Davis Hunter C. , Wong-Campos J. David , Fan Linlin Z. , Gmeiner Benjamin , Begum Shahinoor , Werley Christopher A. , Borja Gabriel B. , Upadhyay Hansini , Shah Himali , Jacques Jane , Park Pojeong , Qi Yitong , Parot Vicente , Deisseroth Karl , Cohen Adam E. 
Published: November 2021

AbstractAll-optical electrophysiology can be a powerful tool for studying neural dynamics in vivo, as it offers the ability to image and perturb membrane voltage in multiple cells simultaneously. The “Optopatch” constructs combine a red-shifted archaerhodopsin (Arch)-derived genetically encoded voltage indicator (GEVI) with a blue-shifted channelrhodopsin actuator (ChR). We used a video-based pooled screen to evolve Arch-derived GEVIs with improved signal-to-noise ratio (QuasAr6a) and kinetics (QuasAr6b). By combining optogenetic stimulation of individual cells with high-precision voltage imaging in neighboring cells, we mapped inhibitory and gap junction-mediated connections, in vivo. Optogenetic activation of a single NDNF-expressing neuron in visual cortex Layer 1 significantly suppressed the spike rate in some neighboring NDNF interneurons. Hippocampal PV cells showed near-synchronous spikes across multiple cells at a frequency significantly above what one would expect from independent spiking, suggesting that collective inhibitory spikes may play an important signaling role in vivo. By stimulating individual cells and recording from neighbors, we quantified gap junction coupling strengths. Together, these results demonstrate powerful new tools for all-optical microcircuit dissection in live mice.
Influence of different anionic charges in lead compoundsin the remediation of lead byEleusine indica (Gaertn)
Authors: Ikhajiagbe B. , Ehiarinmwian R. I. , Omoregie G.O. 
Published: November 2021

AbstractThe study was carried out to investigate the remediative capacity of Eleusine indica in lead-polluted soil. Soil samples were collected near student hostel (hall 5) in the University of Benin. The soil samples were sun dried to constant weight and was pulverized with wooden roller and sieved with a hand sieve of 2 mm mesh size. The sieved soil was spiked with 0.625 g lead nitrate (PbNO3), lead sulphate (PbSO4), lead carbonate (PbCO3), lead acetetrahydrate (PbC2H6) and lead chloride (PbCl2) separately in three replicate using aqueous standard solutions. Tillers of Eleusine Indica were placed in the metal – polluted soil immediately and the experiment was allowed to stay for 15 weeks. The result showed that the uptake efficiency for Eleusineindica in both shoots and roots for lead nitrate was 0.016% and 0.8%, lead sulphate 0.016 % and 0.352 %, lead carbonate 0.064% and 0.496 %, lead acetetrahydrate 0.032 % and 0.688 %, and lead chloride 0.08 % and 0.72 % respectively, indicating that the plant might have sequestered the metal in the soil rather than accumulating it in the leaves. This was evident in the presentation of the metal sequestration factor of over 70 % irrespective of the nature of the metal. Microbial count of soil before and after contamination with lead nitrate was 1.9×104 and 0.4×104 cfu/g indicating a reduction. The study therefore revealed that Eleusine indica is a high efficient plant in sequestering lead in polluted soil.
EZH2 inhibition in glioblastoma stem cells increases the expression of neuronal genes and the neuronal developmental regulators ZIC2, ZNF423 and MAFB
Authors: Kader Bnar Abdul , Distefano Rebecca , West Katherine L. , West Adam G. 
Published: November 2021

AbstractGlioblastoma multiforme (GBM) is an aggressive brain cancer with a very poor prognosis. It has been shown that GBM stem cells within a GBM tumour have increased resistance to standard therapies, so new approaches are needed to increase the range of treatment options available. Here we use two GBM stem cell lines, representing the classical/pro-neural and mesenchymal GBM subtypes, to investigate the effects of three different EZH2 inhibitors on GBM stem cell survival and gene expression: EPZ6438, GSK343 and UNC1999. EZH2 is the catalytic component of the PRC2 chromatin repressor complex, which represses transcription through methylation of histone H3 at lysine 27. Both cell lines showed significantly reduced colony formation after 48-hour exposure to the inhibitors, indicating they were sensitive to all three EZH2 inhibitors. RNA-seq analysis revealed that all three EZH2 inhibitors led to increased expression of genes related to neurogenesis and/or neuronal structure in both GBM stem cell lines. Chromatin immunoprecipitation (ChIP-Seq) was used to identify potential direct targets of the histone methylation activity of EZH2 that might be driving the increase in neuronal gene expression. Three genes were identified as candidate regulatory targets common to both cell lines: MAFB, ZIC2 and ZNF423. These transcription factors all have known roles in regulating neurogenesis, brain development and/or neuronal function. Through analysis of three different EZH2 inhibitors and two GBM stem cell lines, this study demonstrates a common underlying mechanism for how inhibition of EZH2 activity reduces GBM stem cell proliferation and survival.
In vitroassessment of elevated soil iron on germinability and germination characteristics ofSorghum bicolor(L.) Moench after chemo-priming
Authors: Ikhajiagbe Beckley , Onawo Owalum Linus 
Published: November 2021

ABSTRACTThe commercial importance of Sorghum (Sorghum bicolor(L.) Moench) has attracted breeders to increase its seed yield using various breeding approach. Adverse soil factors however hampered progress made in crop development, especially micronutrient toxicity. Plant growth stimulators (PGS) have a significant role in enhancing growth parameters in Sorghum. In the present study, seeds were primed in 50, 150, and 250 ppm of each of gibberellic acid, indole acetic acid, and ascorbic acid respectively for 1 hr before sowing in Petri dishesmoistened with 10 ml of the iron-rich solution obtained as filtrate from a mix of distilled water and ferruginous soil (1:1 v/w). Results showed that although germination percentage in ferruginous medium was significantly reduced, there was enhancement in germination percentagewhen the seeds were primed in gibberellic acid (GA). Germinability in the iron-rich medium was 31.2 hrs; this was significantly reduced to 19.6 to 21.1hrs when these seeds were primed with growth stimulators.Although, shoot length was significantly reduced in plants exposed to ferruginous solutions, the root parameters were however enhanced. They were no significant changes in the total number of root branches regardless of ferrugenic status or use of growth stimulating agents. The utilization of growth stimulators as priming agents is called for to reduce stress impacts imposed by ferruginous soils during germination.
Single-cell dissection of obesity-exercise axis in adipose-muscle tissues
Authors: Yang Jiekun , Vamvini Maria , Nigro Pasquale , Ho Li-Lun , Galani Kiki , Alvarez Marcus , Tanigawa Yosuke , Laakso Markku , Agudelo Leandro , Pajukanta Päivi , Middelbeek Roeland J. W. , Grove Kevin , Goodyear Laurie J. , Kellis Manolis 
Published: November 2021

AbstractRegular physical exercise has long been recognized to reverse the effects of diet-induced obesity, but the molecular mechanisms mediating these multi-tissue beneficial effects remain uncharacterized. Here, we address this challenge by studying the opposing effects of exercise training and high-fat diet at single-cell, deconvolution and tissue-level resolutions across 3 metabolic tissues. We profile scRNA-seq in 204,883 cells, grouped into 53 distinct cell subtypes/states in 22 major cell types, from subcuta-neous and visceral white adipose tissue (WAT), and skeletal muscle (SkM) in mice with diet and exercise training interventions. With a great number of mesenchymal stem cells (MSCs) profiled, we compared depot-specific adipose stem cell (ASC) states, and defined 7 distinct fibro-adipogenic progenitor (FAP) states in SkM including discovering and validating a novel CD140+/CD34+/SCA1-FAP population. Exercise- and obesity-regulated proportion, transcriptional and cell-cell interaction changes were most strongly pronounced in and centered around ASCs, FAPs, macrophages and T-cells. These changes reflected thermogenesis-vs-lipogenesis and hyperplasia-vs-hypertrophy shifts, clustered in pathways including extracellular matrix remodeling and circadian rhythm, and implicated complex single- and multi-tissue communication including training-associated shift of a cytokine from binding to its decoy receptor on ASCs to true receptor on M2 macrophages in vWAT. Overall, our work provides new insights on the metabolic protective effects of exercise training, uncovers a previously-underappreciated role of MSCs in mediating tissue-specific and multi-tissue effects, and serves as a model for multitissue single-cell analyses in physiologically complex and multifactorial traits exemplified by obesity and exercise training.
Comprehensive annotation of 3′UTRs from primary cells and their quantification from scRNA-seq data
Authors: Fansler Mervin M. , Mitschka Sibylle , Mayr Christine 
Published: November 2021

AbstractApproximately half of human genes generate mRNA isoforms that differ in their 3′UTRs while encoding the same protein. 3′UTR and mRNA length is determined by 3′ end cleavage sites (CS). Here, we mapped and categorized mRNA 3′ end CS in more than 200 primary human and mouse cell types, resulting in a 40% increase of CS annotations relative to the GENCODE database. We incorporated these annotations into a novel computational pipeline, called scUTRquant, for rapid, precise, and accurate quantification of gene and 3′UTR isoform expression from single-cell RNA sequencing (scRNA-seq) data. When applying scUTRquant to data from 474 cell types and 2,134 perturbations, we discovered extensive 3′UTR length changes across cell types that are as widespread and dynamically regulated as gene expression changes. Our data indicate that mRNA abundance and mRNA length are two independent axes of gene regulation that together determine the amount and spatial organization of protein synthesis.