bluuebunny/crossref_metadata_2025_split huggingface dataset:
3D bioprinted white adipose model for in vitro study of cancer-associated cachexia induced adipose tissue remodeling
Authors: Xue Wen , Yu Seok-Yeong , Kuss Mitchell , Kong Yunfan , Shi Wen , Chung Soonkyu , Kim So-Youn , Duan Bin 
Published: May 2022

Abstract
Cancer-associated cachexia (CAC) is a complex metabolic and behavioral syndrome with multiple manifestations that involve systemic inflammation, weight loss, and adipose lipolysis. It impacts the quality of life of patients and is the direct cause of death in 20%–30% of cancer patients. The severity of fat loss and adipose tissue remodeling negatively correlate with patients’ survival outcomes. To address the mechanism of fat loss and design potential approaches to prevent the process, it will be essential to understand CAC pathophysiology through white adipose tissue models. In the present study, an engineered human white adipose tissue (eWAT) model based on three-dimensional (3D) bioprinting was developed and induced with pancreatic cancer cell-conditioned medium (CM) to mimic the status of CAC in vitro. We found that the CM induction significantly increased the lipolysis and accumulation of the extracellular matrix (ECM). The 3D eWATs were further vascularized to study the influence of vascularization on lipolysis and CAC progression, which was largely unknown. Results demonstrated that CM induction improved the angiogenesis of vascularized eWATs (veWATs), and veWATs demonstrated decreased glycerol release but increased UCP1 expression, compared to eWATs. Many unique inflammatory cytokines (IL-8, CXCL-1, GM-CSF, etc) from the CM were detected and supposed to contribute to eWAT lipolysis, UCP1 up-regulation, and ECM development. In response to CM induction, eWATs also secreted inflammatory adipokines related to the metastatic ability of cancer, muscle atrophy, and vascularization (NGAL, CD54, IGFBP-2, etc). Our work demonstrated that the eWAT is a robust model for studying cachectic fat loss and the accompanying remodeling of adipose tissue. It is therefore a useful tool for future research exploring CAC physiologies and developing potential therapies.
The influence of heat treatment on the microstructure and corrosion behavior of selective laser melted 316L stainless steel in Ringer’s solution
Authors: Jazaeri Moghadas Seyed Mohammadali , Yeganeh Mahdi , Zaree Seyed Reza Alavi , Eskandari Mostafa 
Published: May 2022

AbstractThe aim of this study is to investigate the effect of heat treatment on the microstructure and corrosion behavior of 316L stainless steel (SS) in Ringer’s solution. The corrosion performance of the as-received, heat-treated at 450 °C (HT1), and 1050 °C (HT2) SS alloys manufactured by selective laser melting was evaluated. The heat treatment at 450 °C and 1050 °C relieved about 38% and 62% of the compressive residual stress derived from the selective laser melting (SLM) process, respectively. The charge transfer resistance of the as-received, HT1, and HT2 was 102, 140, and 12 kΩ cm2in the Ringer’s solution, respectively. This severe reduction in corrosion resistance for the HT2 sample can be attributed to the high possibility of harmful phases such as MnS forming during heat treatment and possibly depletion of chromium content in the inclusions compared to the alloy matrix.
Evaluation of TRPS1 Expression in Pleural Effusion Cytology Specimens With Metastatic Breast Carcinoma
Authors: Wang Minhua , Stendahl Kristin , Cai Guoping , Adeniran Adebowale , Harigopal Malini , Gilani Syed M 
Published: May 2022

Abstract

Objectives
Recent studies have shown that trichorhinophalangeal syndrome type 1 (TRPS1) is a sensitive and specific marker that shows positive staining in breast carcinoma. We conducted this study to evaluate the role of TRPS1 immunohistochemistry (IHC) in differentiating breast primary vs tumors from other primary sites in malignant pleural effusion cytology specimens (MPECSs).

Methods
We selected 61 MPECS cases with cell block material available to analyze TRPS1 IHC staining. Of these 61 cases, 38 cases were metastatic carcinoma (MC) from a breast primary. We primarily selected MC cases confirmed as breast origin based on GATA binding protein 3 IHC positivity, except in two of the cases. The remaining 23 MPECS cases were from various primary sites, including urothelial (n = 6), Müllerian (n = 6), lung adenocarcinoma (n = 6), malignant melanoma (MM; n = 3), and squamous cell carcinoma (SqCC; n = 2).

Results
TRPS1 expression was observed in 35 (92%) of 38 MCs of breast origin. The staining intensity was variable, with 18 (47%) cases showing strong nuclear expression. In comparison, no TRPS1 expression was seen in any cases of urothelial carcinoma, MM, and SqCC. However, four of six Müllerian MC cases demonstrated TRPS1 expression.

Conclusions
TRPS1 is a new marker that can be used in an IHC panel to investigate breast origin in MPECS.
Clinical Validation of a Novel T-Cell Receptor Sequencing Assay for Identification of Recent or Prior Severe Acute Respiratory Syndrome Coronavirus 2 Infection
Authors: Dalai Sudeb C , Dines Jennifer N , Snyder Thomas M , Gittelman Rachel M , Eerkes Tera , Vaney Pashmi , Howard Sally , Akers Kipp , Skewis Lynell , Monteforte Anthony , Witte Pamela R , Wolf Cristina , Nesse Hans , Herndon Megan , Qadeer Jia , Duffy Sarah , Svejnoha Emily , Taromino Caroline , Kaplan Ian M , Alsobrook John , Manley Thomas , Baldo Lance 
Published: May 2022

Abstract

Background
While diagnostic, therapeutic, and vaccine development in the coronavirus disease 2019 (COVID-19) pandemic has proceeded at unprecedented speed, critical gaps in our understanding of the immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remain unaddressed by current diagnostic strategies.

Methods
A statistical classifier for identifying prior SARS-CoV-2 infection was trained using &gt;4000 SARS-CoV-2–associated T-cell receptor (TCR) β sequences identified by comparing 784 cases and 2447 controls from 5 independent cohorts. The T-Detect COVID (Adaptive Biotechnologies) assay applies this classifier to TCR repertoires sequenced from blood samples to yield a binary assessment of past infection. Assay performance was assessed in 2 retrospective (n = 346; n = 69) and 1 prospective cohort (n = 87) to determine positive percent agreement (PPA) and negative percent agreement (NPA). PPA was compared with 2 commercial serology assays, and pathogen cross-reactivity was evaluated.

Results
T-Detect COVID demonstrated high PPA in individuals with prior reverse transcription–polymerase chain reaction (RT-PCR)–confirmed SARS-CoV-2 infection (97.1% 15+ days from diagnosis; 94.5% 15+ days from symptom onset), high NPA (∼100%) in presumed or confirmed SARS-CoV-2 negative cases, equivalent or higher PPA than 2 commercial serology tests, and no evidence of pathogen cross-reactivity.

Conclusions
T-Detect COVID is a novel T-cell immunosequencing assay demonstrating high clinical performance for identification of recent or prior SARS-CoV-2 infection from blood samples, with implications for clinical management, risk stratification, surveillance, and understanding of protective immunity and long-term sequelae.
Idiopathic nephrotic syndrome relapse following COVID-19 vaccination: a series of 25 cases
Authors: Hummel Aurélie , Oniszczuk Julie , Kervella Delphine , Charbit Marina , Guerrot Dominique , Testa Angelo , Philipponnet Carole , Chauvet Cécile , Guincestre Thomas , Brochard Karine , Benezech Ariane , Figueres Lucile , Belenfant Xavier , Guarnieri Andrea , Demoulin Nathalie , Benetti Elisa , Miglinas Marius , Dessaix Kathleen , Morelle Johann , Angeletti Andrea , Sellier-Leclerc Anne-Laure , Ranchin Bruno , Goussard Guillaume , Hudier Laurent , Bacchetta Justine , Servais Aude , Audard Vincent 
Published: May 2022

ABSTRACT

Background
Several cases of idiopathic nephrotic syndrome (INS) relapse following the administration of coronavirus disease 2019 (COVID-19) vaccines have recently been reported, raising questions about the potential relationship between the immune response to COVID-19 vaccination and INS pathogenesis.

Methods
We performed a retrospective multicentre survey describing the clinical and biological characteristics of patients presenting a relapse of INS after COVID-19 vaccination, with an assessment of outcome under treatment.

Results
We identified 25 patients (16 men and 9 women) presenting a relapse within 1 month of a COVID-19 vaccine injection. The glomerular disease was of childhood onset in half of the patients and most patients (21/25) had received at least one immunosuppressive drug in addition to steroids for frequently relapsing or steroid-dependent nephrotic syndrome (NS). All patients were in a stable condition at the time of injection and 11 had no specific treatment. In five patients, the last relapse was reported &gt;5 years before vaccine injection. The Pfizer-BioNTech (BNT162b2) vaccine was used in 80% of the patients. In 18 cases, INS relapse occurred after the first injection, a mean of 17.5 days after vaccination. A second injection was nevertheless administered in 14 of these patients. Five relapses occurred after administration of the second dose and two relapses after the administration of the third dose. All but one of the patients received steroids as first-line treatment, with an additional immunosuppressive agent in nine cases. During follow-up, complete remission was achieved in 21 patients, within 1 month in 17 cases. Only one patient had not achieved at least partial remission after 3 months of follow-up.

Conclusions
This case series suggests that, in rare patients, COVID-19 vaccination may trigger INS relapse that is generally easy to control. These findings should encourage physicians to persuade their patients to complete the COVID-19 vaccination schedule.
Comparative Risk of Incident Cancer in Patients with Inflammatory Bowel Disease with Prior Non-digestive Malignancy According to Immunomodulator: a Multicentre Cohort Study
Authors: Poullenot F , Amiot A , Nachury M , Viennot S , Altwegg R , Bouhnik Y , Abitbol V , Nancey S , Vuitton L , Peyrin-Biroulet L , Biron A , Fumery M , Picon L , Vidon M , Reenaers C , Serrero M , Savoye G , Beaugerie L , Rivière P , Laharie D 
Published: May 2022

Abstract

Introduction
Knowledge about the cancer risk when initiating a biologic in inflammatory bowel disease [IBD] patients with prior malignancy remains scarce, especially for vedolizumab. Our aim was to evaluate the rate of incident cancer in a cohort of IBD patients with prior non-digestive malignancy, according to the subsequent treatment given.

Methods
A multicentre retrospective study included consecutive IBD patients with prior non-digestive malignancy. Inclusion date corresponded to the diagnosis of index malignancy. Patients were categorized into different cohorts according to the first treatment [none, conventional immunosuppressant, anti-TNF, or vedolizumab] to which they were exposed after inclusion and before incident cancer [recurrent or new cancer].

Results
Among the 538 patients {58% female; mean (standard deviation [SD]) age inclusion: 52 [15] years} analyzed, the most frequent malignancy was breast cancer [25%]. The first immunomodulator given after inclusion was a conventional immunosuppressant in 27% of patients, anti-TNF in 21%, or vedolizumab in 9%. With a median (interquartile range [IQR]) follow-up duration of 55 [23-100] months, 100 incident cancers were observed. Crude cancer incidence rates per 1000 person-years were 47.0 for patients receiving no immunomodulator, 36.6 in the anti-TNF cohort, and 33.6 in the vedolizumab cohort [p = 0.23]. Incident-cancer free survival rates were not different between patients receiving anti-TNF and those receiving vedolizumab [p = 0.56]. After adjustment, incidence rates were not different between patients receiving no immunomodulator, anti-TNF, or vedolizumab.

Conclusions
In this large multicentre cohort study, there was no difference of cancer incidence in those IBD patients with prior non-digestive malignancy, treated with vedolizumab or anti-TNF.
What We Talk About When We Talk About “Junk DNA”
Authors: Fagundes Nelson J.R. , Bisso-Machado Rafael , Figueiredo Pedro I.C.C. , Varal Maikel , Zani André L.S. 
Published: May 2022

Abstract
“Junk DNA” is a popular yet controversial concept that states that organisms carry in their genomes DNA that has no positive impact on their fitness. Nonetheless, biochemical functions have been identified for an increasing fraction of DNA elements traditionally seen as “Junk DNA”. These findings have been interpreted as fundamentally undermining the “Junk DNA” concept. Here, we reinforce previous arguments that this interpretation relies on an inadequate concept of biological function that does not consider the selected effect of a given genomic structure, which is central to the “Junk DNA” concept. Next, we suggest that another (though ignored) confounding factor is that the discussion about biological functions includes two different dimensions: a horizontal, ecological dimension that reflects how a given genomic element affects fitness in a specific time, and a vertical, temporal dimension that reflects how a given genomic element persisted along time. We suggest that “Junk DNA” should be used exclusively relative to the horizontal dimension, while for the vertical dimension, we propose a new term, “Spam DNA”, that reflects the fact that a given genomic element may persist in the genome even if not selected for on their origin. Importantly, these concepts are complementary. An element can be both “Spam DNA” and “Junk DNA”, and “Spam DNA” can also be recruited to perform evolved biological functions, as illustrated in processes of exaptation or constructive neutral evolution.
Haploid and Sexual Selection Shape the Rate of Evolution of Genes across the Honey Bee (Apis melliferaL.) Genome
Authors: Slater Garett P. , Dapper Amy L. , Harpur Brock A. 
Published: May 2022

AbstractMany species have separate haploid and diploid phases. Theory predicts that each phase should experience the effects of evolutionary forces (like selection) differently. In the haploid phase, all fitness-affecting alleles are exposed to selection, whereas in the diploid phase, those same alleles can be masked by homologous alleles. This predicts that selection acting on genes expressed in haploids should be more effective than diploid-biased genes. Unfortunately, in arrhenotokous species, this prediction can be confounded with the effects of sex-specific expression, as haploids are usually reproductive males. Theory posits that, when accounting for ploidal- and sex-specific expression, selection should be equally efficient on haploid- and diploid-biased genes relative to constitutive genes. Here, we used a multiomic approach in honey bees to quantify the evolutionary rates of haploid-biased genes and test the relative effects of sexual- and haploid-expression on molecular evolution. We found that 16% of the honey bee’s protein-coding genome is highly expressed in haploid tissue. When accounting for ploidy and sex, haploid- and diploid-biased genes evolve at a lower rate than expected, indicating that they experience strong negative selection. However, the rate of molecular evolution of haploid-biased genes was higher than diploid-based genes. Genes associated with sperm storage are a clear exception to this trend with evidence of strong positive selection. Our results provide an important empirical test of theory outlining how selection acts on genes expressed in arrhenotokous species. We propose the haploid life history stage affects genome-wide patterns of diversity and divergence because of both sexual and haploid selection.
In patients undergoing oesophagectomy does postoperative home enteral nutrition have any impact on nutritional status?
Authors: Li Xiaokun , Hu Jianrong , Zhou Jianfeng , Fang Pinhao , Yuan Yong 
Published: May 2022

Summary
A best evidence topic in thoracic surgery was written according to a structured protocol. The question addressed was ‘In patients undergoing oesophagectomy does postoperative home enteral nutrition have any impact on nutritional status?’ Altogether, 50 articles were found using the reported search, of which 5 studies represented the best evidence to answer the clinical question. This consisted of 1 systematic review including a meta-analysis of 9 randomized controlled trials (RCTs), 3 RCTs and 1 cohort study. Main outcomes included loss of body weight and body mass index (BMI), change of serum albumin, haemoglobin, total protein and prealbumin, rates of nutritional risk patients and score value of patient-generated subjective global assessment. The meta-analysis concluded that there were significant differences in the loss of body weight and BMI between 2 groups, with higher values observed in the HEN group than that in the control group. One RCT showed that patients receiving HEN had a significantly lower weight loss compared with the control group. However, in another RCT, there was no significant difference between 2 groups in the loss of weight and body BMI. The available evidence shows that patients receiving home enteral nutrition yielded a significantly better BMI and lower decrease in body weight than those without after surgical resection of oesophageal cancer. We conclude that HEN could serve as an effective intervention for patients undergoing oesophagectomy. Moreover, the optimal time for patients receiving HEN could be 4–8 weeks after discharge. Feeding via jejunostomy and nasointestinal tube are feasible and safety approaches for HEN.
SARS-CoV-2 Virus Dynamics in Recently Infected People—Data From a Household Transmission Study
Authors: Mellis Alexandra M , Meece Jennifer K , Halasa Natasha B , Chappell James D , McLean Huong Q , Grijalva Carlos G , Hanson Kayla E , Zhu Yuwei , Kim Ahra , Deyoe Jessica , Ivacic Lynn C , Reed Carrie , Talbot H Keipp , Rolfes Melissa A 
Published: May 2022

Abstract
We used daily real-time reverse-transcription polymerase chain reaction (RT-PCR) results from 67 cases of SARS-CoV-2 infection in a household transmission study, conducted April 2020–May 2021, to examine the trajectory of cycle threshold (Ct) values, an inverse correlate of viral RNA concentration. Ct values varied across RT-PCR platforms and by participant age. Specimens collected from children and adolescents had higher Ct values and adults aged ≥50 years showed lower Ct values than adults aged 18–49 years. Ct values were lower on days when participants reported experiencing symptoms, with the lowest Ct value occurring 2–6 days after symptom onset.
Impact of Coronavirus Disease 2019 (COVID-19) Severity on Long-term Events in United States Veterans Using the Veterans Affairs Severity Index for COVID-19 (VASIC)
Authors: Galloway Ashley , Park Yojin , Tanukonda Vidisha , Ho Yuk-Lam , Nguyen Xuan-Mai T , Maripuri Monika , Dey Andrew T , Gerlovin Hanna , Posner Daniel , Lynch Kristine E , Cai Tianxi , Luoh Shiuh-Wen , Whitbourne Stacey , Gagnon David R , Muralidhar Sumitra , Tsao Phillip S , Casas Juan P , Gaziano J Michael , Wilson Peter W F , Hung Adriana M , Cho Kelly 
Published: May 2022

Abstract
In this retrospective cohort study of 94 595 severe acute respiratory syndrome coronavirus 2–positive cases, we developed and validated an algorithm to assess the association between coronavirus disease 2019 (COVID-19) severity and long-term complications (stroke, myocardial infarction, pulmonary embolism/deep vein thrombosis, heart failure, and mortality). COVID-19 severity was associated with a greater risk of experiencing a long-term complication 31–120 days postinfection. Most incident events occurred 31–60 days postinfection and diminished after day 91, except heart failure for severe patients and death for moderate patients, which peaked on days 91–120. Understanding the differential impact of COVID-19 severity on long-term events provides insight into possible intervention modalities and critical prevention strategies.
Two Concepts of Groove: Musical Nuances, Rhythm, and Genre
Authors: Malone Evan 
Published: May 2022

Abstract
Groove, as a musical quality, is an important part of jazz and pop music appreciative practices. Groove talk is widespread among musicians and audiences, and considerable importance is placed on generating and appreciating grooves in music. However, musicians, musicologists, and audiences use groove attributions in a variety of ways that do not track one consistent underlying concept. I argue that there at least two distinct concepts of groove. On one account, the groove is “the feel of the music” and, on the other, the groove is the psychological feeling (induced by music) of wanting to move one’s body. Further, I argue that recent work in music psychology shows that these two concepts do not converge on a unified set of musical features. Finally, I also argue that these two concepts play different functional roles in the appreciative practices of jazz and popular music. This should cause us to further consider the mediating role genre plays for aesthetic concepts and provides us with a reason for adopting a more communitarian approach to aesthetics that is attentive to the ways in which aesthetic discourse serves the practices of different audiences.
Development and Validation of a Quantitative Method for Multiple Allergen Detection in Food Using Concatemer-Based Isotope Dilution Mass Spectrometry
Authors: Gavage Maxime , Van Vlierberghe Kaatje , Dieu Marc , Renard Patsy , Arnould Thierry , De Loose Marc , Gevaert Kris , Gillard Nathalie , Van Poucke Christof 
Published: May 2022

Abstract

Background
Accurate food labeling is essential to protect allergic consumers. However, allergen contaminations may occur during the whole food production process. Reliable, sensitive, and robust methods for detecting multiple allergens in food are needed.

Objective
This work aims to develop and validate an LC coupled to tandem mass spectrometry (MS/MS) method for the detection and quantification of hazelnuts, peanuts, milk, and eggs in processed food products.

Methods
In-house-produced incurred test materials, cookies and chocolates, were used for the method development and validation. The quantification was based on the standard addition strategy using qualified reference materials as allergen protein standards and an innovative stable isotope-labeled concatemer as an internal standard.

Results
A method targeting 19 allergen-specific peptides was developed and validated in two laboratories, which strengthens its robustness. The AOAC INTERNATIONAL performance requirements for repeatability, intermediate precision, reproducibility, and recovery were reached for at least one peptide per allergen across both matrixes, and quantification limits complied with the action levels of the Food Industry Guide to the Voluntary Incidental Trace Allergen Labelling (VITAL®) Program Version 3.0.

Conclusion
The combination of incurred test materials, standard addition strategy, and stable isotope-labeled concatemer as an internal standard allowed us to develop and validate a robust method for detecting and quantifying multiple allergens in food with sufficient sensitivity to protect allergic consumers.

Highlights
The combination of characterized incurred test material, calibration with certified reference material, a single stable isotope labelled concatemer and cross-lab validation result in the required standardization and harmonization in food allergen detection according to the stakeholders’ group to assess the robustness of our method.