bluuebunny/crossref_metadata_2025_split huggingface dataset:
jSRC: a flexible and accurate joint learning algorithm for clustering of single-cell RNA-sequencing data
Authors: Wu Wenming , Liu Zaiyi , Ma Xiaoke 
Published: December 2020

Abstract
Single-cell RNA-sequencing (scRNA-seq) explores the transcriptome of genes at cell level, which sheds light on revealing the heterogeneity and dynamics of cell populations. Advances in biotechnologies make it possible to generate scRNA-seq profiles for large-scale cells, requiring effective and efficient clustering algorithms to identify cell types and informative genes. Although great efforts have been devoted to clustering of scRNA-seq, the accuracy, scalability and interpretability of available algorithms are not desirable. In this study, we solve these problems by developing a joint learning algorithm [a.k.a. joints sparse representation and clustering (jSRC)], where the dimension reduction (DR) and clustering are integrated. Specifically, DR is employed for the scalability and joint learning improves accuracy. To increase the interpretability of patterns, we assume that cells within the same type have similar expression patterns, where the sparse representation is imposed on features. We transform clustering of scRNA-seq into an optimization problem and then derive the update rules to optimize the objective of jSRC. Fifteen scRNA-seq datasets from various tissues and organisms are adopted to validate the performance of jSRC, where the number of single cells varies from 49 to 110 824. The experimental results demonstrate that jSRC significantly outperforms 12 state-of-the-art methods in terms of various measurements (on average 20.29% by improvement) with fewer running time. Furthermore, jSRC is efficient and robust across different scRNA-seq datasets from various tissues. Finally, jSRC also accurately identifies dynamic cell types associated with progression of COVID-19. The proposed model and methods provide an effective strategy to analyze scRNA-seq data (the software is coded using MATLAB and is free for academic purposes; https://github.com/xkmaxidian/jSRC).
GutBalance: a server for the human gut microbiome-based disease prediction and biomarker discovery with compositionality addressed
Authors: Yang Fenglong , Zou Quan , Gao Bo 
Published: December 2020

Abstract
The compositionality of the microbiome data is well-known but often neglected. The compositional transformation pertains to the supervised learning of microbiome data and is a critical step that decides the performance and reliability of the disease classifiers. We value the excellent performance of the distal discriminative balance analysis (DBA) method, which selects distal balances of pairs and trios of bacteria, in addressing the classification of high-dimensional microbiome data. By applying this method to the species-level abundances of all the disease phenotypes in the GMrepo database, we build a balance-based model repository for the classification of human gut microbiome–related diseases. The model repository supports the prediction of disease risks for new sample(s). More importantly, we highlight the concept of balance-disease associations rather than the conventional microbe-disease associations and develop the human Gut Balance-Disease Association Database (GBDAD). Each predictable balance for each disease model indicates a potential biomarker-disease relationship and can be interpreted as a bacteria ratio positively or negatively correlated with the disease. Furthermore, by linking the balance-disease associations to the evidenced microbe-disease associations in MicroPhenoDB, we surprisingly found that most species-disease associations inferred from the shotgun metagenomic datasets can be validated by external evidence beyond MicroPhenoDB. The balance-based species-disease association inference will accelerate the generation of new microbe-disease association hypotheses in gastrointestinal microecology research and clinical trials. The model repository and the GBDAD database are deployed on the GutBalance server, which supports interactive visualization and systematic interrogation of the disease models, disease-related balances and disease-related species of interest.
The Human Immunodeficiency Virus (HIV) Index: Using a Patient-Reported Outcome on Engagement in HIV Care to Explain Suboptimal Retention in Care and Virologic Control
Authors: Christopoulos Katerina A , Neilands Torsten B , Koester Kimberly A , Sauceda John A , Dilworth Samantha E , Mugavero Michael J , Crane Heidi M , Fredericksen Rob J , Cachay Edward R , Mayer Kenneth H , Moore Richard D , Napravnik Sonia , Johnson Mallory O 
Published: December 2020

Abstract

Background
We investigated the prospective association between a brief self-report measure of engagement in human immunodeficiency virus (HIV) care (the Index of Engagement in HIV Care; hereafter “Index”) and suboptimal retention and viral suppression outcomes.

Methods
The Centers for AIDS Research Network of Integrated Clinical Systems cohort study combines medical record data with patient-reported outcomes from 8 HIV clinics in the United States, which from April 2016 to March 2017 included the 10-item Index. Multivariable logistic regression was used to estimate the risk and odds ratios of mean Index scores on 2 outcomes in the subsequent year: (1) not keeping ≥75% of scheduled HIV care appointments; and (2) for those with viral suppression at Index assessment, having viral load &gt;200 copies/mL on ≥1 measurement. We also used generalized linear mixed models (GLMMs) to estimate the risk and odds ratios of appointment nonattendance or unsuppressed viral load at any given observation. We generated receiver operating characteristic curves for the full models overlaid with the Index as a sole predictor.

Results
The mean Index score was 4.5 (standard deviation, 0.6). Higher Index scores were associated with lower relative risk of suboptimal retention (n = 2576; logistic regression adjusted risk ratio [aRR], 0.88 [95% confidence interval, .87–.88]; GLMM aRR, 0.85 [.83–.87]) and lack of sustained viral suppression (n = 2499; logistic regression aRR, 0.75 [.68–.83]; GLMM aRR, 0.74 [.68–.80]). The areas under the receiver operating characteristic curve for the full models were 0.69 (95% confidence interval, .67–.71) for suboptimal retention and 0.76 (.72–.79) for lack of sustained viral suppression.

Conclusions
Index scores are significantly associated with suboptimal retention and viral suppression outcomes.
Outcomes in Previously Healthy Cryptococcal Meningoencephalitis Patients Treated With Pulse Taper Corticosteroids for Post-infectious Inflammatory Syndrome
Authors: Anjum Seher , Dean Owen , Kosa Peter , Magone M Teresa , King Kelly A , Fitzgibbon Edmond , Kim H Jeff , Zalewski Chris , Murphy Elizabeth , Billioux Bridgette Jeanne , Chisholm Jennifer , Brewer Carmen C , Krieger Chantal , Elsegeiny Waleed , Scott Terri L , Wang Jing , Hunsberger Sally , Bennett John E , Nath Avindra , Marr Kieren A , Bielekova Bibiana , Wendler David , Hammoud Dima A , Williamson Peter 
Published: December 2020

Abstract

Background
Cryptococcal meningoencephalitis (CM) is a major cause of mortality in immunosuppressed patients and previously healthy individuals. In the latter, a post-infectious inflammatory response syndrome (PIIRS) is associated with poor clinical response despite antifungal therapy and negative cerebrospinal fluid (CSF) cultures. Data on effective treatment are limited.

Methods
Between March 2015 and March 2020, 15 consecutive previously healthy patients with CM and PIIRS were treated with adjunctive pulse corticosteroid taper therapy (PCT) consisting of intravenous methylprednisolone 1 gm daily for 1 week followed by oral prednisone 1 mg/kg/day, tapered based on clinical and radiological response plus oral fluconazole. Montreal cognitive assessments (MOCA), Karnofsky performance scores, magnetic resonance imaging (MRI) brain scanning, ophthalmic and audiologic exams, and CSF parameters including cellular and soluble immune responses were compared at PIIRS diagnosis and after methylprednisolone completion.

Results
The median time from antifungal treatment to steroid initiation was 6 weeks. The most common symptoms at PIIRS diagnosis were altered mental status and vision changes. All patients demonstrated significant improvements in MOCA and Karnofsky scores at 1 month (P &lt; .0003), which was accompanied by improvements in CSF glucose, white blood cell (WBC) count, protein, cellular and soluble inflammatory markers 1 week after receiving corticosteroids (CS) (P &lt; .003). All patients with papilledema and visual field deficits also exhibited improvement (P &lt; .0005). Five out of 7 patients who underwent audiological testing demonstrated hearing improvement. Brain MRI showed significant improvement of radiological findings (P = .001). CSF cultures remained negative.

Conclusions
PCT in this small cohort of PIIRS was associated with improvements in CM-related complications with minimal toxicity in the acute setting.
A case report of an unusual left atrial mass
Authors: Udemgba Chinelo , Missov Emil , Percy Robert , Sattiraju Srinivasan 
Published: December 2020

Abstract

Background
Cardiac foreign bodies (FBs) are rare findings that may present as cardiac masses initially. Here, we present an exceptional and rare case of a hypodermic needle FB that transmigrated to the left atrium and presented as a left atrial mass.

Case summary
A 28-year-old woman with multiple psychiatric disorders including intentional FB ingestion and self-inflicting injuries presented to the emergency room with abdominal pain, nausea, vomiting, diarrhoea, and chest pain that radiated to the left arm and face for 2 weeks. An echocardiogram was performed revealing a left atrial mass concerning for myxoma. During the surgical removal of the mass, a hypodermic needle was found attached to the roof of the left atrium surrounded by thrombotic and fibrotic tissue, which was confirmed by pathology.

Discussion
Cardiac FBs are caused generally by penetrating wounds from direct trauma. Fewer cases have been reported regarding cardiac FB caused by ingestion from migration of the object to the heart. Signs and symptoms for cardiac FB may mimic those of cardiac masses. Cardiac FBs often require surgical intervention to avoid complications.
Transcatheter aortic valve implantation with a novel pre-packaged self-expandable dry-tissue transcatheter aortic valve: a case report
Authors: Jose John , George Paul V , V. Krishnaprasath , Sahajanandan Raj 
Published: December 2020

Abstract

Background
Current commercially available transcatheter aortic valves are stored separately in a glutaraldehyde solution and mounted onto the delivery system by a technical expert during the transcatheter aortic valve implantation (TAVI) procedure. A pre-mounted dry-tissue valve that is crimped on a ready-to-use delivery system could simplify the procedure. The Vienna self-expanding transcatheter valve (P&F, GmbH, Wessling, Germany) is a novel ready-to-use pre-mounted dry-tissue transcatheter aortic valve. There are no prior reports on the efficacy of this valve system.

Case summary
Here, we report our experience of an implantation of a novel ready-to-use dry-tissue Vienna transcatheter aortic valve in a 72-year-old male with symptomatic severe aortic stenosis and severe left ventricular systolic dysfunction. He had presented with heart failure [N-terminal pro-brain natriuretic peptide (NT-proBNP) level at the admission of 10 600 pg/mL], New York Heart Association Class-3, and recurrent syncope. A 26 mm Vienna valve was successfully implanted via the transfemoral route under conscious sedation. There were no complications. The patient was discharged in a stable condition on the third post-procedure day. At 1-year follow-up, the valve is functioning well with no evidence of structural degeneration (mean gradient 9 mmHg, no valvular regurgitation). Currently, he is asymptomatic with normal left ventricular systolic function on echocardiography (NT-proBNP 57 pg/mL).

Discussion
To our knowledge, this is the first case of TAVI performed with the dry-tissue pre-mounted VIENNA valve. Our case highlights the feasibility and short-term efficacy of the VIENNA valve. Further safety and durability need to be addressed by a multicentre trial.
Does the Injunction Gap Violate Implementers’ Fair Trial Rights Under the ECHR?
Authors: Dijkman Léon E 
Published: December 2020

Abstract
Germany is one of few jurisdictions with a bifurcated patent system, under which infringement and validity of a patent are established in separate proceedings. Because validity proceedings normally take longer to conclude, it can occur that remedies for infringement are imposed before a decision on the patent’s validity is available. This phenomenon is colloquially known as the ‘injunction gap’ and has been the subject of increasing criticism over the past years.
In this article, I examine the injunction gap from the perspective of the right to a fair trial enshrined in Art. 6 of the European Convention on Human Rights. I find that the case law of the European Court of Human Rights interpreting this provision supports criticism of the injunction gap, because imposing infringement remedies with potentially far-reaching consequences before the validity of a patent has been established by a court of law arguably violates defendants’ right to be heard. Such reliance on the patent office’s grant decision is no longer warranted in the light of contemporary invalidation rates. I conclude that the proliferation of the injunction gap should be curbed by an approach to a stay of proceedings which is in line with the test for stays as formulated by Germany’s Federal Supreme Court. Under this test, courts should stay infringement proceedings until the Federal Patent Court or the EPO’s Board of Appeal have ruled on the validity of a patent whenever it is more likely than not that it will be invalidated.
Modeling the transmission of the new coronavirus in São Paulo State, Brazil—assessing the epidemiological impacts of isolating young and elder persons
Authors: Mo Yang Hyun , Pedro Lombardi Junior Luis , Campos Yang Ariana 
Published: December 2020

AbstractWe developed a mathematical model to describe the new coronavirus transmission in São Paulo State, Brazil. The model divided a community into subpopulations composed of young and elder persons considering a higher risk of fatality among elder persons with severe CoViD-19. From the data collected in São Paulo State, we estimated the transmission and additional mortality rates. Based on the estimated model parameters, we calculated the basic reproduction number $R_{0}$, and we retrieved the number of deaths due to CoViD-19, which was three times lower than those found in the literature. Considering isolation as a control mechanism, we varied the isolation rates in the young and elder subpopulations to assess the epidemiological impacts. The epidemiological scenarios focused mainly on evaluating the reduction in the number of severe CoViD-19 cases and deaths due to this disease when isolation is introduced in a population.
Performance Characteristics of a Rapid Severe Acute Respiratory Syndrome Coronavirus 2 Antigen Detection Assay at a Public Plaza Testing Site in San Francisco
Authors: Pilarowski Genay , Lebel Paul , Sunshine Sara , Liu Jamin , Crawford Emily , Marquez Carina , Rubio Luis , Chamie Gabriel , Martinez Jackie , Peng James , Black Douglas , Wu Wesley , Pak John , Laurie Matthew T , Jones Diane , Miller Steve , Jacobo Jon , Rojas Susana , Rojas Susy , Nakamura Robert , Tulier-Laiwa Valerie , Petersen Maya , Havlir Diane V , DeRisi Joseph 
Published: December 2020

Abstract
We evaluated the performance of the Abbott BinaxNOW rapid antigen test for coronavirus disease 2019 (Binax-CoV2) to detect virus among persons, regardless of symptoms, at a public plaza site of ongoing community transmission. Titration with cultured severe acute respiratory syndrome coronavirus 2 yielded a human observable threshold between 1.6 × 104-4.3 × 104 viral RNA copies (cycle threshold [Ct], 30.3–28.8). Among 878 subjects tested, 3% (26 of 878) were positive by reverse-transcription polymerase chain reaction, of whom 15 of 26 had a Ct &lt;30, indicating high viral load; of these, 40% (6 of 15) were asymptomatic. Using this Ct threshold (&lt;30) for Binax-CoV2 evaluation, the sensitivity of Binax-CoV2 was 93.3% (95% confidence interval, 68.1%–99.8%) (14 of 15) and the specificity was 99.9% (99.4%–99.9%) (855 of 856).
Impact of Fasting Status on the Use of Klotho as a Biomarker
Authors: Paquette Jean-Sébastien , Gerard Ngueta , Djade Codjo Djignefa , Cadrin-Chênevert Alexandre , Martel Elise , Boudreault Samuel , Pelletier Mathieu 
Published: December 2020

Abstract

Background
Klotho is a protein secreted physiologically in humans. It acts like a hormone that regulates many biological processes. It is also a novel serological biomarker that is increasingly used as a predictive factor for several physiological and psychological conditions. Surprisingly, there is no consensus about the fasting state of the patient who is tested for klotho. Most studies are done on fasting patients, although others are done without concern about fasting status. There is a lack of evidence about this variable in klotho serological testing. Performing fasting tests on patients can be deleterious and can affect compliance. We investigated the effect of fasting status on klotho serological value.

Methods
We conducted an observational study in which klotho serology was evaluated in a fasting state and 2 h after a meal. In total, 35 participants came to the laboratory without having eaten for 10 h. Blood samples were taken on arrival at our laboratory and 2 h after eating a standardized meal.

Results
The mean age of our participants was 32.7 years old. There were 13 men and 22 women. In the fasting state, the klotho value was 1060.5 pg/mL (SD: 557.5 pg/mL). At 2 h after the meal, the klotho value was 1077.5 pg/mL (SD: 576.9 pg/mL). Statistical tests showed no difference before and after a meal in our study (P = 0.2425).

Conclusions
Our results suggest that it is not necessary to perform klotho serology in a fasting state.
A high-throughput phenotyping algorithm is portable from adult to pediatric populations
Authors: Geva Alon , Liu Molei , Panickan Vidul A , Avillach Paul , Cai Tianxi , Mandl Kenneth D 
Published: December 2020

Abstract

Objective
Multimodal automated phenotyping (MAP) is a scalable, high-throughput phenotyping method, developed using electronic health record (EHR) data from an adult population. We tested transportability of MAP to a pediatric population.

Materials and Methods
Without additional feature engineering or supervised training, we applied MAP to a pediatric population enrolled in a biobank and evaluated performance against physician-reviewed medical records. We also compared performance of MAP at the pediatric institution and the original adult institution where MAP was developed, including for 6 phenotypes validated at both institutions against physician-reviewed medical records.

Results
MAP performed equally well in the pediatric setting (average AUC 0.98) as it did at the general adult hospital system (average AUC 0.96). MAP’s performance in the pediatric sample was similar across the 6 specific phenotypes also validated against gold-standard labels in the adult biobank.

Conclusions
MAP is highly transportable across diverse populations and has potential for wide-scale use.
Impact of Agro-industrial Byproducts on Bioconversion, Chemical Composition, in vitro Digestibility, and Microbiota of the Black Soldier Fly (Diptera: Stratiomyidae) Larvae
Authors: Galassi Gianluca , Jucker Costanza , Parma Pietro , Lupi Daniela , Crovetto Gianni Matteo , Savoldelli Sara , Colombini Stefania 
Published: December 2020

Abstract
The interest in using byproducts from agro-food industries as a rearing substrate for insects is increasing rapidly. We investigated the influence of byproducts of vegetal origin (okara—a byproduct of soy milk production, maize distillers with solubles, brewer’s grains), used as rearing diet for black soldier fly larvae (BSFL), on the following parameters: biomass production, substrate reduction (SR), nutritional profile and in vitro digestibility, and larval gut microbiota. Hen diet was used as a control substrate. The highest larval biomass was collected on maize distillers, whereas the highest SR was observed on okara. The rearing substrate affected ash, ether extract, and chitin larval content. The BSFL reared on okara were characterized by a lower lauric acid content (17.6% of total fatty acids). Diets also influenced in vitro crude protein digestibility (%) for monogastrics, with the highest values for BSFL reared on maize distillers (87.8), intermediate for brewer’s grains and okara BSFL, and the lowest for hen BSFL (82.7). The nutritive value for ruminants showed a lower Net Energy for lactation for BSFL reared on hen diet than okara and dried maize distillers BSFL. The different byproducts showed an influence on the larval gut microbiota, with a major bacterial complexity observed on larvae fed with the hen diet. The neutral detergent fiber concentration of dietary substrate was negatively correlated with Firmicutes and Actinobacteria relative abundance. Insects valorized byproducts converting them into high-value larval biomass to be used for feed production. The results evidenced the effects of the tested byproducts on the measured parameters, underling the chemical composition importance on the final insect meal quality.
CAP Analysis of the Distribution of the Introduced Bemisia tabaci (Hemiptera: Aleyrodidae) Species Complex in Xinjiang, China and the Southerly Expansion of the Mediterranean Species
Authors: Jia Zunzun , Fu Kaiyun , Guo Wenchao , Jiang Weihua , Ahmat Tursun , Ding Xinhua , He Jiang , Wang Xiaowu 
Published: December 2020

Abstract
Bemisia tabaci (Gennadius) cryptic complex has invaded Xinjiang, China, since 1998. The distribution of Mediterranean (MED) and Middle East-Asia Minor 1 (MEAM1) B. tabaci substrains has been gradually identified due to the development of molecular technology. In this study, the distribution of MED and MEAM1 in Xinjiang was determined by cleaved amplified polymorphic sequence (CAPs). Results showed that MED dominated in northern Xinjiang (84%), whereas MEAM1 was dominant in southern Xinjiang (72%). Five pairs of simple sequence repeat (SSR) primers were used to analyze the genetic diversity of B. tabaci among 36 geographic populations. The genetic diversity of MED and MEAM1was low and varied little among populations in Xinjiang (0.09 ± 0.14 and 0.09 ± 0.13, respectively). Based on ∆K statistic, 13 populations of MEAM1 could be classified into two subgroups at K = 2, whereas the 23 populations of MED could be classified into four subgroups at K = 4. However, Mantel t-test demonstrated no correlation between geographical and genetic distances among B. tabaci complex (R = 0.42, P = 1.00). Neighbor-joining and principal coordinate analysis showed that geographical isolation and interspecific differences were the main causes of the genetic variation. Gene flow predicted that MEAM1 was most likely introduced from Urumqi to the southern Xinjiang. Meanwhile, a large proportion of MED in Kashi region came from Changji and Yining. To block ongoing dispersal, strict detection and flower quarantine regulations need to be enforced.