bluuebunny/crossref_metadata_2025 huggingface dataset:
Use of a Comprehensive 66-Gene Cholestasis Sequencing Panel in 2171 Cholestatic Infants, Children, and Young Adults
Authors: Karpen Saul J. , Kamath Binita M. , Alexander John J. , Ichetovkin Ilia , Rosenthal Philip , Sokol Ronald J. , Dunn Shelley , Thompson Richard J. , Heubi James E.
Published: March 2021

Objectives:

Cholestasis is caused by a wide variety of etiologies, often genetic in origin. Broad overlap in clinical presentations, particularly in newborns, renders prioritizing diagnostic investigations challenging. In this setting, a timely, comprehensive assessment using a multigene panel by a clinical diagnostic laboratory would likely prove useful. We summarize initial findings from a testing program designed to discover genetic causes of cholestasis.

Methods:

A neonatal/adult sequencing panel containing 66 genes (originally 57; nine added March 2017) relevant to cholestasis was used. A broad range of eligible patients were enrolled with current/history of cholestasis without an identified cause, or unexplained chronic liver disease. DNA sequencing utilized a custom-designed capture library, and variants were classified and reported as benign, likely benign, variant of unknown significance (VOUS), likely pathogenic (LP), or pathogenic (P), according to the clinical interpretation workflow at EGL Genetics (Tucker, GA).

Results:

A total of 2433 samples were submitted between February 2016 and December 2017; 2171 results were reported. Median turnaround time was 21 days. Results from the 2171 subjects (57% <1 year old) included 583 P variants, 79 LP variants, and 3117 VOUS; 166 P/LP variants and 415 VOUS were novel. The panel's overall diagnostic yield was 12% (n = 265/2171) representing 32 genes. The top five genetic diagnoses for the group, in order: JAG1 + NOTCH2 (Alagille syndrome), ABCB11, SERPINA1, ABCB4, and POLG.

Conclusions:

These findings support the utility of comprehensive rapid multigene testing in diagnosing cholestasis and highlight the evolving understanding of genetic variants contributing to the pathogenesis of cholestasis.
Pediatric Non‐Alcoholic Fatty Liver Disease Is Affected by Genetic Variants Involved in Lifespan/Healthspan
Authors: Crudele Annalisa , Dato Serena , Re Oriana Lo , Maugeri Andrea , Sanna Paola , Giallongo Sebastiano , Oben Jude , Panera Nadia , De Rango Francesco , Mosca Antonella , Rose Giuseppina , Passarino Giuseppe , Alisi Anna , Vinciguerra Manlio
Published: March 2021

Objectives:

Non‐alcoholic fatty liver disease (NAFLD) is the leading cause of chronic liver disease in both adults and children. Along with obesity and metabolic syndrome, genetic predisposition influences the progression of NAFLD. Here, we investigated the effect of lifespan/healthspan‐related single nucleotide polymorphisms (SNPs) on metabolically associated fatty liver disease in children.

Methods:

We evaluated the impact of 10 SNPs involved in both human liver/metabolic diseases and healthspan (interleukin‐6 [IL‐6] rs1800795, antisense non coding RNA in the INK4 locus (ANRIL) rs1556516, SH2B3/ATXN2 rs7137828, FURIN rs17514846, TP53 rs1042522, APOC3 rs2542052, KL rs9536314, KL rs9527025, SIRT6 rs107251, FOXO3 rs2802292) on NAFLD‐related metabolic and liver features in 177 pediatric patients with biopsy‐proven NAFLD, by comparing them to 146 healthy controls. We then applied a multidimensional reduction (MDR) case–control analysis of SNP–SNP interactions, to identify the joint effect of analyzed SNPs in predicting NAFLD and associated features.

Results:

Discrete SNPs were significantly associated with individual metabolic NAFLD features, but none of them significantly associated with NAFLD diagnosis. By testing potential synergies using the MDR approach, the best combination to diagnose NAFLD (P = 0.0011) resulted in the one encompassing IL‐6 rs1800795 and ANRIL rs1556516. Consistently, the risk combinations suggested by SNP–SNP analysis strongly associated with a higher level of fasting plasma blood glucose level (P = 0.024).

Conclusion:

In conclusion, here we demonstrated a synergic interaction between IL‐6 rs1800795 and ANRIL rs1556516 in the diagnosis of NAFLD, and NAFLD‐associated hyperglycemia in children. Larger studies are required to confirm our findings and to elucidate mechanisms by which the genetic interaction between these two genes influences healthspan in pediatric NAFLD.
Fixation Using Alternative Implants for the Treatment of Hip Fractures
Authors: Sprague Sheila , Bhandari Mohit , Bzovsky Sofia , Scott Taryn , Thabane Lehana , Heels-Ansdell Diane , O’Toole Robert V. , Howe Andrea , Gaski Greg E. , Hill Lauren C. , Brown Krista M. , Viskontas Darius , Zomar Mauri , Della Rocca Gregory J. , Slobogean Gerard P.
Published: March 2021

Objectives:

To conduct a pilot trial for the Fixation using Alternative Implants for the Treatment of Hip Fractures (FAITH-2) protocol to assess feasibility of a definitive trial.

Design:

Pilot trial.

Setting:

Twenty-five clinical sites across North America and Australia were initiated, but enrolment occurred in only 15 North American sites.

Patients/Participants:

Ninety-one randomized adults aged 18 to 60 years with a femoral neck fracture requiring surgical fixation.

Intervention:

Eligible patients were randomized to receive surgical treatment (sliding hip screw or cancellous screws) AND nutritional supplementation (4000 IU of vitamin D or placebo) for 6 months postfracture.

Main Outcome Measurements:

Feasibility outcomes included: clinical site initiation, participant enrolment rate, proportion of participants with complete 12-month follow-up, level of data quality, and rate of protocol adherence (number of randomization errors, crossovers between treatment groups, and daily supplementation adherence).

Results:

Eighty-six of 91 participants randomized into the pilot trial from 15 North American hospitals were deemed eligible. Four of five primary feasibility criteria were not achieved as we were unable to initiate clinical sites outside of North America and Australia due to feasibility constraints, slow participant enrolment (60 participants recruited over 36 mo), low adherence with daily nutritional supplementation at the 6-week (72.1%), 3-month (60.5%), and 6-month (54.7%) follow-up visits, and a high loss to follow-up rate of 22.1% at 12 months.

Conclusions:

Despite not meeting key feasibility criteria, we increased our knowledge on the logistics and anticipated barriers when conducting vitamin D supplementation trials in this trauma population, which can be used to inform the design and conduct of future trials on this topic.
Orthopaedic trauma care during a pandemic: initial responses in the United States and Canada
Authors: Swenning Todd , Coles Chad P.
Published: March 2021

As in other countries, COVID-19 had a significant impact on the delivery of Orthopaedic trauma care in North America. Both Canada and the United States had similar experiences and responses to the pandemic, while the burden of disease was significantly greater in the United States. There was significant uncertainty in the early phases of the pandemic, fueled by a lack of knowledge of the pathophysiology and spread of COVID-19, questions surrounding screening protocols, lack of guidelines for managing infected patients, and concern over limited supplies of personal protective equipment. As we gained knowledge and experience, changes were implemented to optimize the delivery of trauma care, some of which may have lasting effects. In this article, we share the experiences and lessons learned in Canada and the United States in response to the pandemic.
Orthopaedic trauma care during the COVID-19 Pandemic: the Latin American perspective
Authors: Padilla-Rojas Luis G. , López-Cervantes Roberto E. , López-Almejo Leonardo , Gutiérrez-Mendoza Israel , Amadei-Enghelmayer Rafael E. , Pesciallo César A. , Osma-Rueda José L. , Triana-Quijano Miguel A. , Santos-Silva Jorge Dos
Published: March 2021

At first glance, the COVID-19 pandemic and the field of orthopaedics and traumatology do not appear to be related. Although orthopaedists are not considered front-line personnel in the fight against the pandemic, the role of the surgeon as part of the overall health care team is crucial. The specialty of orthopaedics and orthopaedic trauma, due to its extraordinary scope, affects individuals of all ages and timely care affects patients’ long-term function and quality of life. Therefore, positioning the type and timing of care for musculoskeletal injuries and conditions, while maintaining the safety of the patient and healthcare providers, is essential. This article reviews the initial approaches to orthopaedic trauma care during the COVID-19 pandemic as established by 4 representative countries in Latin America: Mexico, Argentina, Colombia, and Brazil.
Orthopaedic trauma care: initial global approaches to management during a pandemic
Authors: Miclau Theodore
Published: March 2021

The coronavirus disease 2019 (COVID-19) has significantly affected the treatment of patients with surgical conditions, including those with acute and chronic musculoskeletal issues. While different global regions experienced different levels of COVID-19 activity and had different resources with which to deal with the pandemic, there were many consistent approaches to injury care and musculoskeletal trauma management. Understanding these approaches is necessary to improve current and future strategies to taking care of orthopaedic trauma patients in an infectious disease outbreak. This supplement focuses on approaches to musculoskeletal trauma care during the first months of the COVID-19 pandemic in 19 countries from 6 continents. This work represents a collaborative work of member societies of the International Orthopaedic Trauma Association (IOTA), an international association of orthopaedic societies dedicated to the promotion of musculoskeletal trauma care through advancements in patient care, research, and education. The information in these reports will aid efforts to understand and ultimately better address musculoskeletal trauma care worldwide during the first waves of the pandemic.
SATB2 Expression in Uterine Sarcoma: A Multicenter Retrospective Study
Authors: Le Page Cécile , Almadani Noorah , Turashvili Gulisa , Bataillon Guillaume , Portelance Lise , Provencher Diane , Mes-Masson Anne-Marie , Gilks Blake , Hoang Lien , Rahimi Kurosh
Published: March 2021

Uterine sarcomas represent a clinical challenge because of their difficult diagnosis and the poor prognosis of certain subtypes. The aim of this study was to evaluate the expression of the special AT-rich sequence-binding protein 2 (SATB2) in endometrial stromal sarcoma (ESS) and other types of uterine sarcoma by immunohistochemistry. We studied the expression of SATB2 on 71 full tissue sections of endometrial stromal nodule, low-grade ESS, uterine leiomyomas and leiomyosarcoma, undifferentiated uterine sarcoma, adenosarcoma, and carcinosarcoma samples. Nuclear SATB2 expression was then evaluated in an extended sample set using a tissue microarray, including 78 additional uterine tumor samples. Overall, with a cut-off of ≥10% of tumor cell staining as positive, the nuclear SATB2 score was negative in all endometrial stromal nodule samples (n=10) and positive in 83% of low-grade ESS samples (n=29/35), 40% of undifferentiated uterine sarcoma (n=4/10), 13% of leiomyosarcoma (n=2/16), 14% of adenosarcoma (n=3/22), and 8% carcinosarcoma (n=2/25) samples. Furthermore, in ESS patients, direct comparison of nuclear SATB2 scores with clinicopathologic parameters and other reported biomarkers such as progesterone receptor and estrogen receptor showed that nuclear SATB2 was associated with PR expression and a decreased risk of disease-specific death (odds ratio=0.06, 95% confidence interval=0.04–0.81, P=0.04). Our data suggest that SATB2 could be a marker with relative sensitivity (83%) for distinguishing between endometrial stromal nodule and ESS with potential prognostic value.
Endometrial Adenocarcinomas With No Specific Molecular Profile: Morphologic Features and Molecular Alterations of “Copy-number Low” Tumors
Authors: Meljen Vivienne T. , Mittenzwei Rhonda , Wong Janice , Puechl Allison , Whitaker Regina , Broadwater Gloria , Hall Allison H. , Bean Sarah M. , Bentley Rex C. , Elvin Julia A. , Berchuck Andrew , Previs Rebecca A. , Strickland Kyle C.
Published: March 2021

The study evaluated morphologic patterns, mutational profiles, and β-catenin immunohistochemistry (IHC) in copy-number low (CNL) endometrial adenocarcinomas (EAs). CNL EAs (n=19) with next-generation or whole genome sequencing results and available tissue for IHC were identified from our institutional database. Clinical data and histologic slides were reviewed. IHC for β-catenin was performed and correlated with mutation status. Images of digital slides of CNL EAs from The Cancer Genome Atlas (TCGA) database (n=90) were blindly reviewed by 4 pathologists, and morphology was correlated with mutation status. Categorical variables were analyzed using the Fisher exact test, and agreement was assessed using Fleiss κ. CTNNB1 mutations were present in 63% (12/19) of CNL EAs. β-catenin nuclear localization was present in 83% of CTNNB1-mutated tumors (10/12) and in 0% (0/7) of CTNNB1-wildtype tumors (sensitivity 0.83, specificity 1.00). Squamous differentiation (SD) was present in 47% (9/19) and was more often observed in CTNNB1-mutated tumors (P=0.02). Mucinous differentiation (MD) was associated with KRAS mutations (P<0.01). Digital image review of TCGA CNL EAs revealed that pathologist agreement on SD was strong (κ=0.82), whereas agreement on MD was weak (κ=0.48). Pathologists identified SD in 22% (20/90), which was significantly associated with the presence of CTNNB1 mutations (P<0.01). CNL EAs demonstrate several morphologies with divergent molecular profiles. SD was significantly associated with CTNNB1 mutations and nuclear localization of β-catenin in these tumors. Nuclear expression of β-catenin is a sensitive and specific IHC marker for CTNNB1 mutations in CNL EAs. CNL EAs with KRAS mutations often displayed MD.
No-Charge Nonsurgical Facial Aesthetic Clinic in a Residency Program
Authors: Kaplan Jordan , Huyhn Anh , Izaddoost Shayan , Grome Luke , Reece Edward , Winocour Julian , Davis Matthew J. , Winocour Sebastian
Published: March 2021

Background

In 2014, the Accreditation Council for Graduate Medical Education set minimum case requirements for injectable procedures as a surrogate for procedural competency. Despite the implementation of resident-run aesthetic surgery clinics, evidence suggests that many feel inadequately prepared as they go into practice even after meeting this requirement. To address this issue, our institution has implemented a separate resident clinic dedicated to neurotoxin and filler injections.

Objective

The authors discussed the logistics and benefits of how residents, faculty, clinic staff, and industry representatives together have created a no-cost, volunteer patient-based resident injectable clinic.

Description

Two half-day, no-cost clinics per week were established, with 1 clinic day coinciding with the chief resident aesthetic clinic. Designated staff coordinate patient visits and allocate specific rooms for this clinic. Industry representatives have provided injectable products at no cost through resident injectable education programs. Residents in postgraduation years 4 to 6 provide their own patients and perform procedures under direct faculty supervision. All encounters are documented in the electronic health record. To assess the utility of this clinic, a survey was sent to all recent graduates, some of whom participated in this program. Since its inception in May 2018, this injectable clinic has been running successfully with overwhelmingly positive feedback from all eligible residents who participated. To date, there have been no adverse events from these injections.

Conclusions

At our institution, the no-cost, volunteer patient-based resident injectable clinic has provided regular educational opportunities for plastic surgery residents to increase their experience with injectable procedures.
Unexpected, mystifying but simple three-dimensional dynamic fracture phenomena
Authors: Uenishi Koji
Published: March 2021

This contribution addresses what can be learnt from our recent experimental observations of dynamic fracture development in brittle solid materials with real three-dimensional configurations. It is pointed out that the three-dimensional dynamic behaviour of (quasi-)brittle solids is essentially different not only from the one-dimensional dynamic one but also from the three-dimensional static one. The experimental observations include those of cylindrical concrete columns pressurized by deflagration at the centre and ice spheres subjected to dynamic impact at the bottom. Surprisingly, plain fracture patterns can be found through these experiments, but it does not seem simple to describe or predict the involved physical process by conventional analytical treatment or numerical simulations. Indeed, our understanding of mechanical details of actual three-dimensional fracture is still limited, especially in dynamic cases where the length scale of fracture and relevant waves is of the order of the size of solids under consideration. Although a more sophisticated physical interpretation including the dynamic interaction of waves in a relatively high-frequency range is required, the discussed dynamics of three-dimensional fracture development will assist in generating precisely controlled dynamic fracture networks that can be used for practical purposes of dismantling solid structural components and mitigating risks of catastrophic failures.

This article is part of the theme issue ‘Fracture dynamics of solid materials: from particles to the globe’.
Earthquake physics beyond the linear fracture mechanics: a discrete approach
Authors: Dȩbski W. , Klejment P.
Published: March 2021

Fast development of seismology and related disciplines like seismic prospecting observed in recent decades has its roots in efficient applications of ideas of continuum media mechanics to describe seismic wave propagation through the Earth. Using the same approach enhanced by fracture mechanics methods to describe physical processes leading to nucleation, development and finally arresting of earthquake ruptures has also advanced our understanding of earthquake physics. However, in this case, we can talk only about a partial success since many aspects of earthquake processes are still very poorly understood if at all. We argue that to progress with seismic source analysis we need to turn our attention to a complementary approach, namely a ‘discrete’ one. We demonstrate here that taking into account discreteness of solid materials we are able not only to incorporate classical ‘continuum’ solutions but also reveal many details of fracture processes whose analysis is beyond the classical fracture mechanics. In this paper, we analyse tensional processes encountered in rock mechanics laboratory experiments, mining seismology and sometimes in realistic inter-plate seismic episodes. The ‘discreteness’ principle is implemented through the discrete element method—the numerical method entirely based on the discrete representation of the medium. Special attention is paid to energy accumulation and transformation during loading and relaxation phases of fragmentation processes.

This article is part of the theme issue ‘Fracture dynamics of solid materials: from particles to the globe’.
Transmission, adaptation and geographical spread of the Pseudomonas aeruginosa Liverpool epidemic strain
Authors: Moore Matthew P. , Lamont Iain L. , Williams David , Paterson Steve , Kukavica-Ibrulj Irena , Tucker Nicholas P. , Kenna Dervla T. D. , Turton Jane F. , Jeukens Julie , Freschi Luca , Wee Bryan A. , Loman Nicholas J. , Holden Stephen , Manzoor Susan , Hawkey Peter , Southern Kevin W. , Walshaw Martin J. , Levesque Roger C. , Fothergill Joanne L. , Winstanley Craig
Published: March 2021

The Liverpool epidemic strain (LES) is an important transmissible clonal lineage of

Pseudomonas aeruginosa

that chronically infects the lungs of people with cystic fibrosis (CF). Previous studies have focused on the genomics of the LES in a limited number of isolates, mostly from one CF centre in the UK, and from studies highlighting identification of the LES in Canada. Here we significantly extend the current LES genome database by genome sequencing 91 isolates from multiple CF centres across the UK, and we describe the comparative genomics of this large collection of LES isolates from the UK and Canada. Phylogenetic analysis revealed that the 145 LES genomes analysed formed a distinct clonal lineage when compared with the wider

P. aeruginosa

population. Notably, the isolates formed two clades: one associated with isolates from Canada, and the other associated with UK isolates. Further analysis of the UK LES isolates revealed clustering by clinic geography. Where isolates clustered closely together, the association was often supported by clinical data linking isolates or patients. When compared with the earliest known isolate, LESB58 (from 1988), many UK LES isolates shared common loss-of-function mutations, such as in genes gltR and fleR. Other loss-of-function mutations identified in previous studies as common adaptations during CF chronic lung infections were also identified in multiple LES isolates. Analysis of the LES accessory genome (including genomic islands and prophages) revealed variations in the carriage of large genomic regions, with some evidence for shared genomic island/prophage complement according to clinic location. Our study reveals divergence and adaptation during the spread of the LES, within the UK and between continents.
Production of high-acidity peach vinegar by improving the
manufacturing process of “Dochobang”
Authors: Jeon Seong-hyun , Park Hyun-Ju , Kim So-Young , Yeo Soo-Hwan , Gwon Hee-Min
Published: March 2021

According to the method described in the ancient literature
“Imwonsipyukji”, ‘Dochobang’ was mainly composed of
lactic acid (756.81 mg/100 mL) and acetic acid (473.66 mg/100 mL) as the main
organic acids on the 14th day of fermentation. The acidity of
‘Dochobang’ was 1.09%, resulting in low marketability.
Therefore, this study aimed to improve the manufacturing process of peach
vinegar and optimize the conditions, including temperature and initial pH, for
producing high-acidity vinegar using fermented seeds. We first selected yeasts
(Saccharomyces cerevisiae YM27) with excellent alcohol
fermentation ability and acetic acid bacteria (Acetobacter
oryzifermentans (KACC19301)) with remarkable acid-producing ability
and used these in the process-improved two-stage fermentation. The experiment
was conducted by 3 treatments of tepmerature(20°C, 30°C and
35°C) and initial pH(3, 4 and 5) for acetic acid fermentation.
‘Dochobang’ fermented alcohol and acetic acid at the same time by
natural fermentation. on the other hand, peach wine starter and seed vinegar
were added before each fermentation step to increase acetic acid production.
Wines fermented at 25°C and 30°C were found to be 9%
alcoholic on days sixth and nine days, respectively. Organic acid analysis
revealed that the level of acetic acid in vinegar fermented at pH 4 and
20°C increased steadily until day 14 (6,171.3 mg/100 mL). The acidity was
7% on the 21st day of fermentation. Furthermore, as the fermentation
progressed, the umami and sourness of the peach vinegar increased. We expect
that our findings could improve the quality of peach vinegar recorded in the old
literature and can be used in small-scale agricultural companies.
Characterization of Lactobacillus paracasei
JSRL18-60 with probiotic properties as a starter in manufacturing fermented
milk
Authors: Jeong Su-Ji , Yang Hee-Jong , Ryu Myeong Seon , Seo Ji Won , Jeong Do-Youn
Published: March 2021

In this study, eighty-eight lactic acid bacteria (LAB) were isolated from Korean
traditional fermented foods for use as yogurt. Among the isolates, thirteen LAB
strains with curd formation ability were selected. Among these, five LAB strains
exhibited notable antibacterial activity against pathogens, such as
Bacillus cereus, Staphylococcus aureus,
and Listeria ivanovii. JSRL18-60 strain showed superior
probiotic properties, such as high adhesion capacity to Caco-2 colorectal
adenocarcinoma cells, and tolerance to low pH, temperature, and condition of the
bile. Based on these results, JSRL18-60 strain was selected for further
evaluation and identified by 16S rRNA sequencing as Lactobacillus
paracasei. The maximum growth of L. paracasei
JSRL18-60 was determined after 30 h of fermentation by measuring the optical
density (1.74), viable cell number (9.61 log CFU/mL), and dried cell weight
(2.30 g/L). Finally, we manufactured fermented milk using skimmed milk and
L. paracasei JSRL18-60, and the optimal pH condition (pH
4.48) of the fermented milk was reached within 21 h of fermentation. Moreover,
the log of the total cell count of L. paracasei JSRL18-60 was
retained for at least 10 days at 9.48-9.36 log CFU/mL. The pH and acidity levels
of the fermented milk containing L. paracasei JSRL18-60 were
changed from pH 4.48 and 0.89% to pH 4.38 and 0.98%, respectively,
in 10 days. These findings suggested that L. paracasei
JSRL18-60 could be used as a starter for producing fermented milk with probiotic
properties.
Changes in flavor ingredients of distilled fruit brandy according
to the aging container and maturation period
Authors: Jung Sangmi , Kwon Minhee , Chung Bonghwan , Ra Moonjin
Published: March 2021

We investigated the effects of container type (oak, glass, and stainless
vessels), maturation period, and application of two different fruit materials
(Actinidia arguta (ChungSan, Korean name), and
Vitis coignetiae (Black Sun, Korean name) cultivated in
Gangwon, Korea) on the flavor characteristics of brandies. After 17 months of
aging, significant changes in the flavor ingredients occurred only in the
brandies matured in oak containers. Particularly, the level of isoamyl alcohol,
an important flavor component, increased, indicating 1,294.3 mg/L and 4,125.4
mg/L in Actinidia arguta brandy respectively, and 898.3 mg/L
and 1,605.6 mg/L in Vitis coignetiae brandy respectively. In
contrast, the levels of acetaldehyde and methanol, which are volatile components
decreased significantly after seven months of aging. In addition, changes in the
brandy flavor based on the maturation period were confirmed by measuring the
proportion of fatty acid ethyl esters. In general, the proportion of fatty acid
ethyl esters increased as the maturation period decreased. Therefore, we found
that the brandy matured in oak containers for all maturation periods was the
most preferable based on the sensory evaluation, which might be correlated with
a balance between the desirable and undesirable components with aging.
Early prediction of preeclampsia in pregnancy with circulating cell-free RNA
Authors: Moufarrej Mira N. , Vorperian Sevahn K. , Wong Ronald J. , Campos Ana A. , Quaintance Cecele C. , Sit Rene V. , Tan Michelle , Detweiler Angela M. , Mekonen Honey , Neff Norma F. , Druzin Maurice L. , Winn Virginia D. , Shaw Gary M. , Stevenson David K. , Quake Stephen R.
Published: March 2021

Liquid biopsies that measure circulating cell-free RNA (cfRNA) offer an unprecedented opportunity to noninvasively study the development of pregnancy-related complications and to bridge gaps in clinical care. Here, we used 404 blood samples from 199 pregnant mothers to identify and validate cfRNA transcriptomic changes that are associated with preeclampsia (PE), a multi-organ syndrome which is the second largest cause of maternal death globally. We find that changes in cfRNA gene expression between normotensive (NT) and preeclamptic mothers are striking and stable early in gestation, well before the onset of symptoms. These changes are enriched for genes specific to neuromuscular, endothelial, and immune cell types and tissues that reflect important aspects of PE physiology and suggest new hypotheses for disease progression. This enabled identification and independent validation of a panel of 18 genes whose measurement between 5–16 weeks of gestation can form the basis of a liquid biopsy test that would identify mothers at risk of PE well before the clinical symptoms manifest themselves. Finally, we demonstrate that cfRNA changes reflect the multifactorial nature of PE and provide a means to non-invasively monitor maternal organ health. Tests based on these observations could help predict and manage who is at risk for PE, an important and until now unachieved objective for obstetric care.
COVID-19 Underreporting and its Impact on Vaccination Strategies
Authors: Albani Vinicius , Loria Jennifer , Massad Eduardo , Zubelli Jorge P.
Published: March 2021

We present a novel methodology for the stable rate estimation of hospitalization and death related to the Corona Virus Disease 2019 (COVID-19) using publicly available reports from various distinct communities. These rates are then used to estimate underreported infections on the corresponding areas by making use of reported daily hospitalizations and deaths. The impact of underreporting infections on vaccination strategies is estimated under different disease-transmission scenarios using a Susceptible-Exposed-Infective-Removed-like (SEIR) epidemiological model.

One sentence Summary

Using a novel methodology, we estimate COVID-19 underreporting from public data, quantifying its impact on vaccination.
Effective Connectivity and Dopaminergic Function of Fronto-Striato-Thalamic Circuitry in First-Episode Psychosis, Established Schizophrenia, and Healthy Controls
Authors: Sabaroedin Kristina , Razi Adeel , Chopra Sidhant , Tran Nancy , Pozaruk Andrii , Chen Zhaolin , Finlay Amy , Nelson Barnaby , Allott Kelly , Alvarez-Jimenez Mario , Graham Jessica , Baldwin Lara , Tahtalian Steven , Yuen Hok P , Harrigan Susy , Cropley Vanessa , Sharma Sujit , Saluja Bharat , Williams Robert , Pantelis Christos , Wood Stephen J. , O’Donoghue Brian , Francey Shona , McGorry Patrick , Aquino Kevin , Fornito Alex
Published: March 2021

Dysfunction of fronto-striato-thalamic (FST) circuits is thought to contribute to dopaminergic dysfunction and symptom onset in psychosis, but it remains unclear whether this dysfunction is driven by aberrant bottom-up subcortical signaling or impaired top-down cortical regulation. Here, we used spectral dynamic causal modelling (DCM) of resting-state functional magnetic resonance imaging (fMRI) to characterize the effective connectivity of dorsal and ventral FST circuits in a sample of 46 antipsychotic-naïve first-episode psychosis (FEP) patients and 23 controls and an independent sample of 36 patients with established schizophrenia (SCZ) patients and 100 controls. We found that midbrain and thalamic connectivity were implicated across both patient groups. Dysconnectivity in FEP patients was mainly restricted to the subcortex, with positive symptom severity being associated with midbrain connectivity. Dysconnectivity between the cortex and subcortical systems was only apparent in SCZ patients. In another independent sample of 33 healthy individuals who underwent concurrent fMRI and [18F]DOPA positron emission tomography, we found that striatal dopamine synthesis capacity was associated with the effective connectivity of nigrostriatal and striatothalamic pathways, implicating similar circuits as those associated with psychotic symptom severity in patients. Our findings thus indicate that subcortical dysconnectivity is salient in the early stages of psychosis, that cortical dysfunction may emerge later in the illness, and that nigrostriatal and striatothalamic signaling are closely related to striatal dopamine synthesis capacity, which is a robust risk marker for psychosis.
Determinants of losses in the latent tuberculosis infection cascade of care in Brazil: a prospective multicenter cohort study
Authors: Souza Alexandra Brito , B. Arriaga María , Amorim Gustavo , Araújo-Pereira Mariana , M. F. Nogueira Betânia , Queiroz Artur T. L. , Figueiredo Marina C. , Rocha Michael S. , Benjamin Aline , Moreira Adriana S. R. , de Oliveira Jamile G. , Rolla Valeria C. , Durovni Betina , Lapa e Silva José R. , Kritski Afrânio L. , Cavalcante Solange , Sterling Timothy R. , Andrade Bruno B. , Cordeiro-Santos Marcelo ,   for the RePORT Brazil consortium
Published: March 2021

Background

Factors associated with losses in the latent tuberculosis infection (LTBI) cascade of care in contacts of tuberculosis (TB) patients were investigated in a multicenter prospective cohort from highly endemic regions in Brazil.

Methods

Close contacts of 1,187 culture-confirmed pulmonary TB patients were prospectively studied between 2015 and 2019, with follow-up between 6 and 24 months. Data on TB screening by clinical investigation, radiographic examination and interferon-gamma release assay (IGRA) were collected. Stepwise multivariable models were used to identify determinants of losses in the LTBI cascade.

Results

Among 4,145 TB contacts initially identified, 1,901 were examined (54% loss). Within those individuals, 933 were people living with HIV, ≤5 years-old and/or had positive IGRA results, therefore having recommendation to start TB preventive treatment (TPT). Of those, 454 (23%) initiated treatment, and 247 (6% of all TB contacts) completed TPT. Multivariable regression analysis revealed that living with HIV, illiteracy, and black/pardo (brown) race were independently associated with losses in cascade.

Conclusion

There were losses at all LTBI cascade stages, but particularly at the initial screening and examination steps. Close contacts who are socially vulnerable and living with HIV were at heightened risk of not completing the LTBI cascade of care in Brazil.

40-word summary of the article’s main point

We investigated factors associated with losses in the latent tuberculosis infection cascade of care in a large cohort of contacts in Brazil. Social vulnerability and HIV infection were the most relevant determinants of losses in the LTBI cascade of care.
Outcome Reporting bias in Exercise Oncology trials (OREO): a cross-sectional study
Authors: Singh Benjamin , Fairman Ciaran M , Christensen Jesper F , Bolam Kate A , Twomey Rosie , Nunan David , Lahart Ian M
Published: March 2021

Background

Despite evidence of selective outcome reporting across multiple disciplines, this has not yet been assessed in trials studying the effects of exercise in people with cancer. Therefore, the purpose of our study was to explore prospectively registered randomised controlled trials (RCTs) in exercise oncology for evidence of selective outcome reporting.

Methods

Eligible trials were RCTs that 1) investigated the effects of at least partially supervised exercise interventions in people with cancer; 2) were preregistered (i.e. registered before the first patient was recruited) on a clinical trials registry; and 3) reported results in a peer-reviewed published manuscript. We searched the PubMed database from the year of inception to September 2020 to identify eligible exercise oncology RCTs clinical trial registries. Eligible trial registrations and linked published manuscripts were compared to identify the proportion of sufficiently preregistered outcomes reported correctly in the manuscripts, and cases of outcome omission, switching, and silently introduction of non-novel outcomes.

Results

We identified 31 eligible RCTs and 46 that were ineligible due to retrospective registration. Of the 405 total prespecified outcomes across the 31 eligible trials, only 6.2% were preregistered complete methodological detail. Only 16% (n=148/929) of outcomes reported in published results manuscripts were linked with sufficiently preregistered outcomes without outcome switching. We found 85 total cases of outcome switching. A high proportion (41%) of preregistered outcomes were omitted from the published results manuscripts, and many published outcomes (n=394; 42.4%) were novel outcomes that had been silently introduced (median, min-max=10, 0-50 per trial). We found no examples of preregistered efficacy outcomes that were measured, assessed, and analysed as planned.

Conclusions

We found evidence suggestive of widespread selective outcome reporting and non-reporting bias (outcome switching, omitted preregistered outcomes, and silently introduced novel outcomes). The existence of such reporting discrepancies has implications for the integrity and credibility of RCTs in exercise oncology.

Preregistered protocol

https://osf.io/dtkar/ (posted: November 19, 2019)
HIV service interruptions during the COVID-19 pandemic in China: the role of HIV service challenges and institutional response from healthcare professional’s perspective
Authors: Yang Xueying , Zeng Chengbo , Tam Cheuk Chi , Qiao Shan , Li Xiaoming , Shen Zhiyong , Zhou Yuejiao
Published: March 2021

Background

The healthcare system in China was largely overwhelmed during the unprecedented pandemic of coronavirus disease (COVID-19). HIV-related services have been unavoidably interrupted and impacted. However, the nature and scope of HIV service interruptions due to COVID-19 has rarely been characterized in China and how HIV service challenges affect the service interruptions are also unclear. The current study aimed at characterize HIV service interruption levels and analyzed its associated factors related to service challenges and institutional response from HIV healthcare providers’ viewpoint.

Methods

A cross-sectional online survey was conducted among 1,029 HIV healthcare providers in Guangxi, China, from April to May 2020. Latent class analysis (LCA) was first used to identify HIV service interruption levels. Then hierarchical multinomial logistic regression was conducted to analyze the relationships of HIV care service challenges and institutional response with HIV service interruption levels. Simple slope analysis was employed to examine interaction effects between HIV service challenges and institutional response to COVID-19.

Results

Four classes of HIV service interruption were identified using LCA, with 22.0% complete interruption (class 1), 15.4% moderate interruption (class 2), 21.9% minor interruption (class 3) and 40.7% almost no interruption (class 4). Using class 4 as a reference group, HIV care service challenges were positively associated with the probabilities of service interruptions (Class 1: AOR=1.23, 95%CI: 1.19∼1.26; Class 2: AOR= 1.10, 95%CI: 1.08∼1.13; Class 3: AOR= 1.10, 95%CI: 1.08∼1.12). Institutional response to HIV healthcare delivery was negatively associated with the probabilities of being classified into Class 1 (“Complete interruption”) (AOR=0.97, 95%CI: 0.93∼1.00) and Class 3 (“minor interruption [Outreach service]”) (AOR=0.96, 95%CI: 0.93∼0.99) as compared to Class 4 (“almost no interruption”). Institutional response to HIV healthcare delivery moderated the association of HIV service challenges with complete interruption, but not with the moderate or minor interruption when comparing with no interruption group.

Conclusions

A substantial HIV service interruptions occurs due to the COVID-19 pandemic, particularly services that require face-to-face interactions, such as VCT counselling, follow up and outreach services. HIV service challenges largely hinder the HIV service delivery. Institutional response to HIV healthcare delivery could marginally buffer the negative effect of service challenges on complete HIV service interruptions. To maintain continuity of core HIV services in face of a pandemic, build a resilient health care system with adequate preparedness is necessary.
Multiplexed single-cell proteomics using SCoPE2
Authors: Petelski Aleksandra A. , Emmott Edward , Leduc Andrew , Huffman R. Gray , Specht Harrison , Perlman David H. , Slavov Nikolai
Published: March 2021

Many biological systems are composed of diverse single cells. This diversity necessitates functional and molecular single-cell analysis. Single-cell protein analysis has long relied on affinity reagents, but emerging mass-spectrometry methods (either label-free or multiplexed) have enabled quantifying over 1,000 proteins per cell while simultaneously increasing the specificity of protein quantification. Isobaric carrier based multiplexed single-cell proteomics is a scalable, reliable, and cost-effective method that can be fully automated and implemented on widely available equipment. It uses inexpensive reagents and is applicable to any sample that can be processed to a single-cell suspension. Here we describe an automated Single Cell ProtEomics (SCoPE2) workflow that allows analyzing about 200 single cells per 24 hours using only standard commercial equipment. We emphasize experimental steps and benchmarks required for achieving quantitative protein analysis.

SCoPE2 Protocol
SARS-CoV-2 Nsp8 N-terminal domain dimerizes and harbors autonomously folded elements
Authors: Treviño Miguel Á. , Pantoja-Uceda David , Laurents Douglas V. , Mompeán Miguel
Published: March 2021

The SARS-CoV-2 Nsp8 protein is a critical component of the RNA replicase, as its N-terminal domain (NTD) anchors Nsp12, the RNA, and Nsp13. Whereas its C-terminal domain (CTD) structure is well resolved, there is an open debate regarding the conformation adopted by the NTD as it is predicted as disordered but found in a variety of complex-dependent conformations or missing from many other structures. Using NMR spectroscopy, we show that the SARS CoV-2 Nsp8 NTD features both well folded secondary structure and disordered segments. Our results suggest that while part of this domain corresponding to two long α-helices forms autonomously, the folding of other segments would require interaction with other replicase components. When isolated, the α-helix population progressively declines towards the C-termini, and dynamics measurements indicate that the Nsp8 NTD behaves as a dimer under our conditions.
Massively parallel characterization of CYP2C9 variant enzyme activity and abundance
Authors: Amorosi Clara J. , Chiasson Melissa A. , McDonald Matthew G. , Wong Lai Hong , Sitko Katherine A. , Boyle Gabriel , Kowalski John P. , Rettie Allan E. , Fowler Douglas M. , Dunham Maitreya J.
Published: March 2021

CYP2C9encodes a cytochrome P450 enzyme responsible for metabolizing up to 15% of small molecule drugs, andCYP2C9variants can alter the safety and efficacy of these therapeutics. In particular, the anti-coagulant warfarin is prescribed to over 15 million people annually and polymorphisms inCYP2C9can affect patient response leading to an increased risk of hemorrhage. We developed Click-seq, a pooled yeast-based activity assay to test thousands of variants. Using Click-seq, we measured the activity of 6,142 missense variants expressed in yeast. We also measured the steady-state cellular abundance of 6,370 missense variants expressed in a human cell line using Variant Abundance by Massively Parallel sequencing (VAMP-seq). These data revealed that almost two-thirds of CYP2C9 variants showed decreased activity, and that protein abundance accounted for half of the variation in CYP2C9 function. We also measured activity scores for 319 previously unannotated human variants, many of which may have clinical relevance.
Ecophysiological differentiation between life stages in filmy ferns (Hymenophyllaceae)
Authors: Nitta Joel H. , Watkins James E. , Holbrook N. Michele , Wang Tristan W. , Davis Charles C.
Published: March 2021

Desiccation tolerance was a key trait that allowed plants to colonize land. However, little is known about the transition from desiccation tolerant non-vascular plants to desiccation sensitive vascular ones. Filmy ferns (Hymenophyllaceae) represent a useful system to investigate how water-stress strategies differ between non-vascular and vascular stages within a single organism because they have vascularized sporophytes and nonvascular gametophytes that are each capable of varying degrees of desiccation tolerance. To explore this, we surveyed sporophytes and gametophytes of 19 species (22 taxa including varieties) of filmy ferns on Moorea (French Polynesia) and used chlorophyll fluorescence to measure desiccation tolerance and light responses. We conducted phylogenetically informed analyses to identify differences in physiology between life stages and growth habits. Gametophytes had similar or less desiccation tolerance (ability to recover from 2 d desiccation at -86 MPa) and lower photosynthetic optima (maximum electron transport rate of photosystem II and light level at 95% of that rate) than sporophytes. Epiphytes were more tolerant of desiccation than terrestrial species in both life stages. Despite their lack of greater physiological tolerances, gametophytes of several species occurred over a wider elevational range than conspecific sporophytes. Our results demonstrate that filmy fern gametophytes and sporophytes differ in their physiology and niche requirements, and point to the importance of microhabitat in shaping the evolution of water-use strategies in vascular plants.
Persisting Salivary IgG against SARS-CoV-2 at 9 Months After Mild COVID-19: A Complementary Approach to Population Surveys
Authors: Alkharaan Hassan , Bayati Shaghayegh , Hellström Cecilia , Olsson Annika , Lindahl Karin , Bogdanovic Gordana , Aleman Soo , Tsilingaridis Georgios , De Palma Patricia , Hober Sophia , Månberg Anna , Nilsson Peter , Pin Elisa , Sällberg Chen Margaret
Published: March 2021

Background

Declining humoral immunity in COVID-19 patients and possibility of reinfections has raised concern. Mucosal immunity particularly salivary antibodies could be short-lived. However, long-term studies are sparse.

Methods

Using a multiplex bead-based array platform, we investigated antibodies specific to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins in 256 saliva samples from convalescent patients 1-9 months after symptomatic COVID-19 (n=74, Cohort 1), undiagnosed individuals with self-reported questionnaires (n=147, Cohort 2), and individuals sampled pre-pandemic time (n= 35, Cohort 3).

Results

Salivary IgG antibody responses in Cohort 1 (mainly mild COVID-19) were detectable up to 9 month recovery, with high correlations between spike and nucleocapsid specificity. At 9 months, IgG remained in saliva in majority as seen in blood serology. Salivary IgA was rarely detected at this timepoint. In Cohort 2, salivary IgG and IgA responses were significantly associated with recent history of COVID-19 like symptoms. Salivary IgG also tolerated temperature and detergent pre-treatments.

Conclusions

Unlike SARS-CoV-2 salivary IgA that appeared short-lived, the specific IgG in saliva appears stable even after mild COVID-19 as noted for blood serology. The non-invasive saliva-based SARS-Cov-2 antibody testing with self-collection at homes may thus serve as a complementary alternative to conventional blood serology.
A Preliminary Characterization of Canonicalized and Non-Canonicalized Section Headers Across Variable Clinical Note Types
Authors: Wang Junjie , Yu Shun , Davoudi Anahita , Mowery Danielle L.
Published: March 2021

In the electronic health record, the majority of clinically relevant information is stored within clinical notes. Most clinical notes follow a set organizational structure composed of canonicalized section headers that facilitate clinical review and information gathering. Standardized section header terminologies such as the SecTag terminology permit the identification and standardization of headers to a canonicalized form. Although the SecTag terminology has been evaluated extensively for history & physical notes, the coverage of canonical section header terms has not been assessed across other note types. For this pilot study, we conducted a coverage study and characterization of canonical section headers across 5 common, clinical note types and a generalizability study of canonical section headers detected within two types of clinical notes from Penn Medicine.