bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reliability and validity of the multidimensional dyspnea profile in hospitalized Chinese patients with respiratory diseases
Authors: Chen Huaying , Li Yamin , Wang Weihong , Zhang Huilin , Nie Na , Ou Jinnan , Li Lezhi 
Published: September 2021

Background: Dyspnea is a multidimensional experience similar to pain and is one of the most common clinical presentations in patients with respiratory diseases. Accurately evaluating the experience of dyspnea allows nurses and physicians to deliver better medical services to patients. The multidimensional dyspnea profile emphasizes the psychosocial factors of dyspnea and assesses immediate discomfort, sensory qualities, and the emotional responses of patients with dyspnea. At present, the validity, reliability, and test–retest reliability of the multidimensional dyspnea profile in patients with respiratory diseases in China are unclear. Objectives: The aim of this study was to investigate the validity, reliability, and test–retest reliability of the Chinese version of the multidimensional dyspnea profile and to assess the convergent validity between the Chinese version of the multidimensional dyspnea profile and the modified Medical Research Council Dyspnea Scale. Methods: The factorial construct, intraclass correlations, internal consistency, and convergent validity of the Chinese version of the multidimensional dyspnea profile was evaluated using data from 231 inpatients with dyspnea from the respiratory department of a hospital. In the principal component analysis stage, 131 inpatients were evaluated. In the test–retest reliability analysis stage, 50 out of the 131 patients responded to the questionnaire again. In the confirmatory factor analysis, 100 inpatients from an independent sample were assessed. Results: The principal component analysis showed that the Chinese version of the multidimensional dyspnea profile had a two-factor structure: the immediate perceptual-related problem factor (6 items) and the emotional response-related problem factor (5 items). The convergent validity between the Chinese version of the multidimensional dyspnea profile and the modified Medical Research Council Dyspnea Scale was significant and acceptable based on the average variance extracted (r = .56, p < .001). The confirmatory factor analysis revealed a good model fit and provided support for the construct validity of the Chinese version of the multidimensional dyspnea profile. Overall, the internal consistency and intraclass correlation coefficient of the Chinese version of the multidimensional dyspnea profile were good. Conclusion: The 11-item Chinese version of the multidimensional dyspnea profile has acceptable validity and reliability in patients with respiratory diseases in China. In the future, more studies should be performed to further explore its clinical application.
Factors Affecting Incidence Rate of Exertional Heat Illnesses: Analysis of 6 Years of High School Football Practices in North Central Florida
Authors: Tripp Brady L. , Winkelmann Zachary K. , Eberman Lindsey E. , Smith Michael Seth 
Published: September 2021

Background: Although experts have advocated for regionally specific heat safety guidelines for decades, guidelines have not been universally adopted. Purpose: To describe the rate and risk factors associated with exertional heat illness (EHI). Study Design: Descriptive epidemiology study. Methods: For a 3-month period (August-October) over 6 years (2013-2018), athletic trainers at 13 high schools in North Central Florida recorded varsity football practice time and length, wet-bulb globe temperature (WBGT), and incidences of EHI, including heat stroke, heat exhaustion, and heat syncope. Results: Athletes sustained 54 total EHIs during 163,254 athlete-exposures (AEs) for the 3-month data collection periods over 6 years (incidence rate [IR], 3.31 /10,000 AEs). Heat exhaustion accounted for 59.3% (32/54), heat syncope 38.9% (21/54), and heat stroke 1.9% (1/54) of all EHIs recorded. Of the EHIs, 94.4% (51/54) were experienced within the first 19 practices. The first 19 practices had an IR of 7.48 of 10,000 AEs, and the remaining 44 practices had an IR of 0.32 of 10,000 AEs, demonstrating that the risk of EHI for practices 1 to 19 was 23.7 times that of the remaining practices. When comparing morning to afternoon practices, 35.2% (19/54) EHI incidents occurred during morning practices. The risk of EHI during practices with WBGT >82°F (27.8°C) was 3.5 times that of practices with WBGT <82°F. Conclusion: In the current study, the risk of EHI was greatest in the first 19 practices of the season and during practices with WBGT >82°F. As modifiable risk factors for EHI, increased vigilance and empowerment to adhere to acclimatization guidelines can mitigate EHI risk. Health care providers must continue to advocate for implementation of regulations and the authority to make decisions to ensure patient safety.
Arthroscopic Fixation of Avulsion Fractures of the Lesser Tuberosity of the Humerus: Clinical Outcomes With a Mean 3.5-Year Follow-up
Authors: Lin Lin , Xiao Jian , Cui Guoqing , Yan Hui 
Published: September 2021

Background: Avulsion fracture of the lesser tuberosity (AFLT) of the humerus has traditionally been treated with open reduction internal fixation using screw fixation. The clinical outcomes of arthroscopic repair with suture anchors remains unknown. Hypothesis: It was hypothesized that arthroscopic fixation with suture anchors would result in good clinical outcomes for the treatment of AFLT. Study Design: Case series; Level of evidence, 4. Methods: This study included 15 patients who underwent arthroscopic repair of AFLT of the humerus between January 2014 and October 2017. All patients had 3-dimensional computed tomography scans and magnetic resonance imaging to evaluate the avulsed fracture and concomitant injuries before surgery. The arthroscopic double-row and suture-bridge techniques were used based on the morphology of the avulsion fractures. Functional outcomes were assessed with range of motion, the visual analog scale (VAS) for pain, the Subjective Shoulder Value (SSV), the American Shoulder and Elbow Surgeons (ASES) score, and the University of California, Los Angeles (UCLA) shoulder score. The bear-hug test, liftoff test, and internal rotation resistance test at 90° abduction and external rotation (IRRT 90°) were used to evaluate subscapularis tendon integrity. Results: The mean follow-up time was 3.5 years (range, 3-5 years). Comminuted fractures with 1 large part and ≥1 small pieces were seen in 12 cases, partial tear of the supraspinatus in 2 cases, Bankart lesion in 2 cases, and superior labrum anterior to posterior injury in 2 cases. There was a statistically significant improvement from the baseline to the final follow-up in the VAS (from 6.9 ± 1.5 to 1.1 ± 1), SSV (from 30.7 ± 5.1 to 90.5 ± 11.6), ASES (from 28.5 ± 7.7 to 92.3 ± 4.5), and UCLA (from 29.5 ± 6.3 to 94.2 ± 8.3) scores ( P < .001 for all). All patients showed full range of shoulder motion and bilateral symmetric strength on physical examination with the bear-hug test, liftoff test, and IRRT 90° test. Conclusion: The arthroscopic repair of AFLT resulted in excellent reduction and healing of the displaced fragment. At the final follow-up, clinical and functional results were good. Associated injuries occurred in 40% of patients but did not affect outcomes.
Optimization of bleaching power by sulfuric acid activation of bentonite
Authors: Bayram Hale , Ustunisik Gokce , Önal Müşerref , Sarıkaya Yüksel 
Published: September 2021

AbstractAcid activation was carried out by heating muds prepared from Ca-rich bentonite (CaB), sulfuric acid (H2SO4) and distilled water, yielding various bleaching earths (BEs). The roles of each of the process variables, namely mass fraction of H2SO4 (x) in the dried CaB and pure H2SO4 mixture, heating temperature (T) and contact time (t), in the activation were tested. The raw CaB and each BE were examined with X-ray diffraction, chemical analyses, N2 adsorption/desorption, pH-metry and tintometry. The BE contents in both the aqueous and oily suspensions were set to 2% by mass in order to measure the pH value and the bleaching power, respectively. The optimum conditions for the activation to obtain a BE having the same bleaching power (0.60) as Tonsil® Optimum Bleaching Earth for soybean oil were determined as x = 0.35, T = 100°C and t = 2 h. The bleaching power increased only marginally upon increasing the activation time from 2 h up to 10 h at a given x and T. After 10 h, significant changes did not take place in the bleaching power of the BE. The mass fraction of total structural metal oxide (y), pH value, specific pore volume (V), specific surface area (S) and mean internal diameter (D) of the mesopores for the optimized BE are y = 0.10, pH = 3.0, V = 0.31 cm3 g–1, S = 225 m2 g–1 and D = 7 nm. The pH and D values were more important for bleaching the alkaline refined soybean oil compared to the other parameters tested.
Detection of clonotypic DNA in the cerebrospinal fluid as a marker of central nervous system invasion in lymphoma
Authors: Olszewski Adam J. , Chorzalska Anna D. , Petersen Max , Ollila Thomas A. , Zayac Adam , Kurt Habibe , Treaba Diana O. , Reagan John L. , Hsu Andrew , Egan Pamela C. , Butera James , Niroula Rabin , Vatkevich John , Robison Jordan , Sahin Ilyas , Jacob Allison P. , Mullins Chelsea D. , Dubielecka Patrycja M. 
Published: September 2021

Abstract
The diagnosis of parenchymal central nervous system (CNS) invasion and prediction of risk for future CNS recurrence are major challenges in the management of aggressive lymphomas, and accurate biomarkers are needed to supplement clinical risk predictors. For this purpose, we studied the results of a next-generation sequencing (NGS)–based assay that detects tumor-derived DNA for clonotypic immunoglobulin gene rearrangements in the cerebrospinal fluid (CSF) of patients with lymphomas. Used as a diagnostic tool, the NGS-minimal residual disease (NGS-MRD) assay detected clonotypic DNA in 100% of CSF samples from 13 patients with known CNS involvement. They included 7 patients with parenchymal brain disease only, whose CSF tested negative by standard cytology and flow cytometry, and 6 historical DNA aliquots collected from patients at a median of 39 months before accession, which had failed to show clonal rearrangements using standard polymerase chain reaction. For risk prognostication, we prospectively collected CSF from 22 patients with newly diagnosed B-cell lymphomas at high clinical risk of CNS recurrence, of whom 8 (36%) had detectable clonotypic DNA in the CSF. Despite intrathecal prophylaxis, a positive assay of CSF was associated with a 29% cumulative risk of CNS recurrence within 12 months of diagnosis, in contrast with a 0% risk among patients with negative CSF (P = .045). These observations suggest that detection of clonotypic DNA can aid in the diagnosis of suspected parenchymal brain recurrence in aggressive lymphoma. Furthermore, the NGS-MRD assay may enhance clinical risk assessment for CNS recurrence among patients with newly diagnosed lymphomas and help select those who may benefit most from novel approaches to CNS-directed prophylaxis.
Symptoms and signs of conjunctivitis as predictors of disease course in COVID-19 syndrome
Authors: Ranzenigo Martina , Bruzzesi Elena , Galli Laura , Castagna Antonella , Ferrari Giulio 
Published: September 2021

Abstract
Background
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can induce conjunctivitis signs and symptoms. However, limited information is available on their impact on COVID-19 disease phenotype. Quantification of ocular signs/symptoms can provide a rapid, non-invasive proxy for predicting clinical phenotype. Moreover, the existence and entity of conjunctival viral shedding is still debated. This has relevant implications to manage disease spread.
The purpose of this study was to investigate conjunctivitis signs and symptoms and their correlation with clinical parameters, conjunctival viral shedding in patients with COVID-19.

Methods
Fifty-three patients hospitalized between February 25th and September 16th, 2020 at the San Raffaele Hospital, in Milan, Lombardy, Italy with a confirmed diagnosis of SARS-CoV-2 were evaluated. Presence of interstitial pneumonia was confirmed with computed tomography scan imaging. Ocular signs and symptoms, anosmia/ageusia, clinical/laboratory parameters, and reverse transcriptase–polymerase chain reaction (RT-PCR) from nasopharyngeal and conjunctival swabs for COVID-19 virus were analyzed.

Results
Forty-six out of 53 patients showed a positive nasopharyngeal swab for SARS-CoV-2 infection at the time of conjunctival evaluation. All the conjunctival swabs were negative. Conjunctivitis symptoms were present in 37% of patients. Physician-assessed ocular signs were detected in 28% of patients.
Patients with ocular symptoms or signs tended to be older: 76.8 years (62.4–83.3) vs 57.2 years (48.1–74.0), p = 0.062 and had a longer hospitalization: 38 days (18–49) vs. 14 days (11–21), p = 0.005. Plasma levels of Interleukin-6 were higher in patients with signs or symptoms in comparison with those without them: 43.5 pg/ml (19.7–49.4) vs. 8 pg/ml (3.6–20.7), p = 0.02. Red cell distribution width was also significantly higher: 15 (14.3–16.7) vs 13.2 (12.4–14.4), p = 0.001.

Conclusions
We found that over a third of the patients had ocular signs or symptoms. These had higher prevalence in patients with a more severe infection. No viral shedding was detected in the conjunctiva. Our results suggest that prompt detection of conjunctivitis signs/symptoms can serve as a helpful proxy to predict COVID-19 clinical phenotype.
Deep GONet: self-explainable deep neural network based on Gene Ontology for phenotype prediction from gene expression data
Authors: Bourgeais Victoria , Zehraoui Farida , Ben Hamdoune Mohamed , Hanczar Blaise 
Published: September 2021

Abstract
Background
With the rapid advancement of genomic sequencing techniques, massive production of gene expression data is becoming possible, which prompts the development of precision medicine. Deep learning is a promising approach for phenotype prediction (clinical diagnosis, prognosis, and drug response) based on gene expression profile. Existing deep learning models are usually considered as black-boxes that provide accurate predictions but are not interpretable. However, accuracy and interpretation are both essential for precision medicine. In addition, most models do not integrate the knowledge of the domain. Hence, making deep learning models interpretable for medical applications using prior biological knowledge is the main focus of this paper.

Results
In this paper, we propose a new self-explainable deep learning model, called Deep GONet, integrating the Gene Ontology into the hierarchical architecture of the neural network. This model is based on a fully-connected architecture constrained by the Gene Ontology annotations, such that each neuron represents a biological function. The experiments on cancer diagnosis datasets demonstrate that Deep GONet is both easily interpretable and highly performant to discriminate cancer and non-cancer samples.

Conclusions
Our model provides an explanation to its predictions by identifying the most important neurons and associating them with biological functions, making the model understandable for biologists and physicians.
Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing
Authors: Jaiswal Sarika , Nandi Samiran , Iquebal Mir Asif , Jasrotia Rahul Singh , Patra Sunita , Mishra Gayatri , Udit Uday Kumar , Sahu Dinesh Kumar , Angadi U. B. , Meher Prem Kumar , Routray Padmanav , Sundaray Jitendra Kumar , Verma Dhananjay Kumar , Das Paramananda , Jayasankar Pallipuram , Rai Anil , Kumar Dinesh 
Published: September 2021

AbstractBackgroundCarp fish, rohu (Labeo rohitaHam.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., post-spawning resting and initiation of gonadal activity appropriate for revealing the associated candidate genes. It can be deciphered by RNA sequencing of tissues involved in BPGL (Brain-Pituitary-Gonad-Liver) axis controlling seasonality. How far such BCGs of this fish are evolutionarily conserved across different phyla is unknown. Such study can be of further use to enhance fish productivity as seasonality restricts seed production beyond monsoon season.ResultA total of ~ 150 Gb of transcriptomic data of four tissues viz., BPGL were generated using Illumina TruSeq.De-novoassembled BPGL tissues revealed 75,554 differentially expressed transcripts, 115,534 SSRs, 65,584 SNPs, 514 pathways, 5379 transcription factors, 187 mature miRNA which regulates candidate genes represented by 1576 differentially expressed transcripts are available in the form of web-genomic resources. Findings were validated by qPCR. This is the first report in carp fish having 32 BCGs, found widely conserved in fish, amphibian, reptile, birds, prototheria, marsupials and placental mammals. This is due to universal mechanism of rhythmicity in response to environment and earth rotation having adaptive and reproductive significance.ConclusionThis study elucidates evolutionary conserved mechanism of photo-periodism sensing, neuroendocrine secretion, metabolism and yolk synthesis in liver, gonadal maturation, muscular growth with sensory and auditory perception in this fish. Study reveals fish as a good model for research on biological clock besides its relevance in reproductive efficiency enhancement.
Culture and genome-based analysis of four soil Clostridium isolates reveal their potential for antimicrobial production
Authors: Pahalagedara Amila S. N. W. , Jauregui Ruy , Maclean Paul , Altermann Eric , Flint Steve , Palmer Jon , Brightwell Gale , Gupta Tanushree Barua 
Published: September 2021

AbstractBackgroundSoil bacteria are a major source of specialized metabolites including antimicrobial compounds. Yet, one of the most diverse genera of bacteria ubiquitously present in soil,Clostridium, has been largely overlooked in bioactive compound discovery. AsClostridiumspp. thrive in extreme environments with their metabolic mechanisms adapted to the harsh conditions, they are likely to synthesize molecules with unknown structures, properties, and functions. Therefore, their potential to synthesize small molecules with biological activities should be of great interest in the search for novel antimicrobial compounds. The current study focused on investigating the antimicrobial potential of four soilClostridiumisolates, FS01, FS2.2 FS03, and FS04, using a genome-led approach, validated by culture-based methods.ResultsConditioned/spent media from all fourClostridiumisolates showed varying levels of antimicrobial activity against indicator microorganism; all four isolates significantly inhibited the growth ofPseudomonas aeruginosa. FS01, FS2.2, and FS04 were active againstBacillus mycoidesand FS03 reduced the growth ofBacillus cereus. Phylogenetic analysis together with DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), and functional genome distribution (FGD) analyses confirmed that FS01, FS2.2, and FS04 belong to the speciesParaclostridium bifermentans,Clostridium cadaveris, andClostridium senegalenserespectively, while FS03 may represent a novel species of the genusClostridium. Bioinformatics analysis using antiSMASH 5.0 predicted the presence of eight biosynthetic gene clusters (BGCs) encoding for the synthesis of ribosomally synthesized post-translationally modified peptides (RiPPs) and non-ribosomal peptides (NRPs) in four genomes. All predicted BGCs showed no similarity with any known BGCs suggesting novelty of the molecules from those predicted gene clusters. In addition, the analysis of genomes for putative virulence factors revealed the presence of four putativeClostridiumtoxin related genes in FS01 and FS2.2 genomes. No genes associated with the mainClostridiumtoxins were identified in the FS03 and FS04 genomes.ConclusionsThe presence of BGCs encoding for uncharacterized RiPPs and NRPSs in the genomes of antagonisticClostridiumspp. isolated from farm soil indicated their potential to produce novel secondary metabolites. This study serves as a basis for the identification and characterization of potent antimicrobials from these soilClostridiumspp. and expands the current knowledge base, encouraging future research into bioactive compound production in members of the genusClostridium.
Phylogenetic analysis and development of molecular markers for five medicinal Alpinia species based on complete plastome sequences
Authors: Yang Heyu , Wang Liqiang , Chen Haimei , Jiang Mei , Wu Wuwei , Liu Shengyu , Wang Jiehua , Liu Chang 
Published: September 2021

Abstract
Background
Alpinia species are widely used as medicinal herbs. To understand the taxonomic classification and plastome evolution of the medicinal Alpinia species and correctly identify medicinal products derived from Alpinia species, we systematically analyzed the plastome sequences from five Alpinia species. Four of the Alpinia species: Alpinia galanga (L.) Willd., Alpinia hainanensis K.Schum., Alpinia officinarum Hance, and Alpinia oxyphylla Miq., are listed in the Chinese pharmacopeia. The other one, Alpinia nigra (Gaertn.) Burtt, is well known for its medicinal values.

Results
The four Alpinia species: A. galanga, A. nigra, A. officinarum, and A. oxyphylla, were sequenced using the Next-generation sequencing technology. The plastomes were assembled using Novoplasty and annotated using CPGAVAS2. The sizes of the four plastomes range from 160,590 bp for A. galanga to 164,294 bp for A. nigra, and display a conserved quadripartite structure. Each of the plastomes encodes a total of 111 unique genes, including 79 protein-coding, 28 tRNA, and four rRNA genes. In addition, 293–296 SSRs were detected in the four plastomes, of which the majority are mononucleotides Adenine/Thymine and are found in the noncoding regions. The long repeat analysis shows all types of repeats are contained in the plastomes, of which palindromic repeats occur most frequently. The comparative genomic analyses revealed that the pair of the inverted repeats were less divergent than the single-copy region. Analysis of sequence divergence on protein-coding genes showed that two genes (accD and ycf1) had undergone positive selection. Phylogenetic analysis based on coding sequence of 77 shared plastome genes resolves the molecular phylogeny of 20 species from Zingiberaceae. In particular, molecular phylogeny of four sequenced Alpinia species (A. galanga, A. nigra, A. officinarum, and A. oxyphylla) based on the plastome and nuclear sequences showed congruency. Furthermore, a comparison of the four newly sequenced Alpinia plastomes and one previously reported Alpinia plastomes (accession number: NC_048461) reveals 59 highly divergent intergenic spacer regions. We developed and validated two molecular markers Alpp and Alpr, based on two regions: petN-psbM and psaJ-rpl33, respectively. The discrimination success rate was 100 % in validation experiments.

Conclusions
The results from this study will be invaluable for ensuring the effective and safe uses of Alpinia medicinal products and for the exploration of novel Alpinia species to improve human health.