bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Characteristics and Outcomes of Immunocompromised Patients With Coronavirus Disease 2019 Caused by the Omicron Variant: A Prospective, Observational Study
Authors: Malahe S Reshwan K , Hoek Rogier A S , Dalm Virgil A S H , Broers Annoek E C , den Hoed Caroline M , Manintveld Olivier C , Baan Carla C , van Deuzen Charlotte M , Papageorgiou Grigorios , Bax Hannelore I , Van Kampen Jeroen J , Hellemons Merel E , Kho Marcia M L , de Vries Rory D , Molenkamp Richard , Reinders Marlies E J , Rijnders Bart J A 
Published: July 2022

Abstract

Background
Illness after infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant is less severe compared with previous variants. Data on the disease burden in immunocompromised patients are lacking. We investigated the clinical characteristics and outcomes of immunocompromised patients with coronavirus disease 2019 (COVID-19) caused by Omicron.

Methods
Organ transplant recipients, patients on anti-CD20 therapy, and allogenic hematopoietic stem cell transplantation recipients infected with the Omicron variant were included. Characteristics of consenting patients were collected and patients were contacted regularly until symptom resolution. To identify possible risk factors for hospitalization, a univariate logistic analysis was performed.

Results
114 consecutive immunocompromised patients were enrolled. Eighty-nine percent had previously received 3 mRNA vaccinations. While only 1 patient died, 23 (20%) were hospitalized for a median of 11 days. A low SARS-CoV-2 immunoglobulin G (IgG) antibody response (&lt;300 BAU [binding antibody units]/mL) at diagnosis, being older, being a lung transplant recipient, having more comorbidities, and having a higher frailty score were associated with hospital admission (all P &lt; .01). At the end of follow-up, 25% had still not fully recovered. Of the 23 hospitalized patients, 70% had a negative and 92% had a low IgG (&lt;300 BAU/mL) antibody response at admission. Sotrovimab was administered to 17 of these patients, and 1 died.

Conclusions
While the mortality in immunocompromised patients infected with Omicron was low, hospital admission was frequent and the duration of symptoms often prolonged. In addition to vaccination, other interventions are needed to limit the morbidity from COVID-19 in immunocompromised patients.
Development of an Effective Immune Response in Adults With Down Syndrome After Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Vaccination
Authors: Esparcia-Pinedo Laura , Yarci-Carrión Ayla , Mateo-Jiménez Gloria , Ropero Noelia , Gómez-Cabañas Laura , Lancho-Sánchez Ángel , Almendro-Vázquez Patricia , Martín-Gayo Enrique , Paz-Artal Estela , Sanchez-Madrid Francisco , Moldenhauer Fernando , Gutiérrez-Cobos Ainhoa , Real de Asúa Diego , Alfranca Arantzazu 
Published: July 2022

Abstract

Background
Immune dysregulation in individuals with Down syndrome (DS) leads to an increased risk for hospitalization and death due to coronavirus disease 2019 (COVID-19) and may impair the generation of protective immunity after vaccine administration.

Methods
The cellular and humoral responses of 55 individuals with DS who received a complete SARS-CoV-2 vaccination regime at 1 to 3 (visit [V 1]) and 6 (V2) months were characterized.

Results
SARS-CoV-2–reactive CD4+ and CD8+ T lymphocytes with a predominant Th1 phenotype were observed at V1 and increased at V2. Likewise, an increase in SARS-CoV-2–specific circulating Tfh (cTfh) cells and CD8+ CXCR5+ PD-1hi lymphocytes was already observed at V1 after vaccine administration. Specific immunoglobulin G (IgG) antibodies against SARS-CoV-2 S protein were detected in 96% and 98% of subjects at V1 and V2, respectively, although IgG titers decreased significantly between both time points.

Conclusions
Our findings show that DS individuals develop an effective immune response to usual regimes of SARS-CoV-2 vaccination.
The regional distinctiveness and variegation of financialisation in emerging economies
Authors: Karwowski Ewa 
Published: July 2022

Abstract
The world region is missing from financialisation analysis of emerging economies (EEs) with little attention given to regional commonalities or comparative analysis across regions. This article sets out to identify regional commonalities in financialisation experiences across EEs, rooted in domestic institutions and countries’ varying integration into the global financial system. Bringing commonalities within and differences between emerging regions to the fore will help us understand the specificities of their political economies and current capitalist experiences. Based on existing research and data availability, six financialisation indicators across five macroeconomic aggregates are identified. Considering 2008–17, a ranking emerges with the most affected region being Central Easter Europe (CEE), followed by Latin America. Emerging Asia takes an intermediate position while EEs in the Middle East and North Africa (MENA) region and Africa show limited signs of financialisation. Our analysis identifies distinct regional features. Financialisation in CEE and Latin America is strongly driven by external forces, the key difference being the role that large domestic capitalists play in the process. Across Emerging Asia, financialisation has mainly unfolded in the private sector while state authorities could to some extent insulate public policy. In MENA, much of the private sector appears outside of the reach of financialisation because of the economic and political power of regional conglomerates. In emerging Africa, the phenomenon is concentrated in very few, if intensely affected, financialisation centres. From a theoretical perspective, we find financialisation is driven by a mix of external factors and domestically influential capitalist elites pursuing their interests.
Financialisation of developing and emerging economies and China’s experience: how China resists financialisation
Authors: Xie Fusheng , Kuang Xiaolu , Li Zhi 
Published: July 2022

Abstract
In this paper, we discuss the process of financialisation of developing countries and emerging economies (DEEs) from the perspective of critical realism (CR). We argue that the emergence of financialisation depends on the inherent tendency of the imbalance between the accumulation of productive and financial capital being actualised, and emphasise how government’s intentional actions under current social structures relate to this process. We use China as a case study to illustrate how DEEs can resist financialisation and maintain productive accumulation during development. We elaborate on various institutional and policy adjustments undertaken by China during different phases that promoted productive accumulation and how China avoided financialisation for much of its growth period. Our discussion helps to explain why China’s limited financialisation compared to other DEEs who experienced financialisation featured by dependency. We conclude by highlighting new potential risks and sources of financialisation faced by the Chinese economy.
Clinical Validation of Genome Reference Consortium Human Build 38 in a Laboratory Utilizing Next-Generation Sequencing Technologies
Authors: Lansdon Lisa A , Cadieux-Dion Maxime , Herriges John C , Johnston Jeffrey , Yoo Byunggil , Alaimo Joseph T , Thiffault Isabelle , Miller Neil , Cohen Ana S A , Repnikova Elena A , Zhang Lei , Farooqi Midhat S , Farrow Emily G , Saunders Carol J 
Published: July 2022

Abstract

Background
Laboratories utilizing next-generation sequencing align sequence data to a standardized human reference genome (HRG). Several updated versions, or builds, have been released since the original HRG in 2001, including the Genome Reference Consortium Human Build 38 (GRCh38) in 2013. However, most clinical laboratories still use GRCh37, which was released in 2009. We report our laboratory’s clinical validation of GRCh38.

Methods
Migration to GRCh38 was validated by comparing the coordinates (lifting over) of 9443 internally curated variants from GRCh37 to GRCh38, globally comparing protein coding sequence variants aligned with GRCh37 vs GRCh38 from 917 exomes, assessing genes with known discrepancies, comparing coverage differences, and establishing the analytic sensitivity and specificity of variant detection using Genome in a Bottle data.

Results
Eight discrepancies, due to strand swap or reference base, were observed. Three clinically relevant variants had the GRCh37 alternate allele as the reference allele in GRCh38. A comparison of 88 295 calls between builds identified 8 disease-associated genes with sequence differences: ABO, BNC2, KIZ, NEFL, NR2E3, PTPRQ, SHANK2, and SRD5A2. Discrepancies in coding regions in GRCh37 were resolved in GRCh38.

Conclusions
There were a small number of clinically significant changes between the 2 genome builds. GRCh38 provided improved detection of nucleotide changes due to the resolution of discrepancies present in GRCh37. Implementation of GRCh38 results in more accurate and consistent reporting.
Child dietary patterns in Homo sapiens evolution
Authors: Iannotti Lora L , Gyimah Emmanuel A , Reid Miranda , Chapnick Melissa , Cartmill Mary Kate , Lutter Chessa K , Hilton Charles , Gildner Theresa E , Quinn Elizabeth A 
Published: July 2022

Abstract
Dietary patterns spanning millennia could inform contemporary public health nutrition. Children are largely absent from evidence describing diets throughout human evolution, despite prevalent malnutrition today signaling a potential genome-environment divergence. This systematic review aimed to identify dietary patterns of children ages 6 months to 10 years consumed before the widespread adoption of agriculture. Metrics of mention frequency (counts of food types reported) and food groups (globally standardized categories) were applied to: compare diets across subsistence modes [gatherer–hunter–fisher (GHF), early agriculture (EA) groups]; examine diet quality and diversity; and characterize differences by life course phase and environmental context defined using Köppen–Geiger climate zones. The review yielded child diet information from 95 cultural groups (52 from GHF; 43 from EA/mixed subsistence groups). Animal foods (terrestrial and aquatic) were the most frequently mentioned food groups in dietary patterns across subsistence modes, though at higher frequencies in GHF than in EA. A broad range of fruits, vegetables, roots and tubers were more common in GHF, while children from EA groups consumed more cereals than GHF, associated with poor health consequences as reported in some studies. Forty-eight studies compared diets across life course phases: 28 showed differences and 20 demonstrated similarities in child versus adult diets. Climate zone was a driver of food patterns provisioned from local ecosystems. Evidence from Homo sapiens evolution points to the need for nutrient-dense foods with high quality proteins and greater variety within and across food groups. Public health solutions could integrate these findings into food-based dietary guidelines for children.
Justification, rationale and methodological approaches to realist reviews
Authors: Pearsons Alice , Neubeck Lis , Hendriks Jeroen M , Hanson Coral L 
Published: July 2022

Abstract
Realist reviews offer a method to understand why an intervention is successful or not. Many factors influence how complex healthcare interventions are delivered and this makes understanding what works difficult. Effectiveness depends on delivery context, and success in one setting does not guarantee the same result in alternate settings. How an intervention works (the underlying mechanisms) in a particular setting for one population group, may not work in the same way for a different group. A realist review provides an iterative theory-driven approach to help understand how and for whom and under what conditions an intervention works.
Imp and Syp mediated temporal patterning of neural stem cells in the developing Drosophila CNS
Authors: Islam Ishrat Maliha , Erclik Ted 
Published: July 2022

Abstract
The assembly of complex neural circuits requires that stem cells generate diverse types of neurons in the correct temporal order. Pioneering work in the Drosophila embryonic ventral nerve cord has shown that neural stem cells are temporally patterned by the sequential expression of rapidly changing transcription factors to generate diversity in their progeny. In recent years, a second temporal patterning mechanism, driven by the opposing gradients of the Imp and Syp RNA-binding proteins, has emerged as a powerful way to generate neural diversity. This long-range temporal patterning mechanism is utilized in the extended neural stem cell lineages of the postembryonic fly brain. Here, we review the role played by Imp and Syp gradients in several neural stem cell lineages, focusing on how they specify sequential neural fates through the post-transcriptional regulation of target genes, including the Chinmo and Mamo transcription factors. We further discuss how upstream inputs, including hormonal signals, modify the output of these gradients to couple neurogenesis with the development of the organism. Finally, we review the roles that the Imp and Syp gradients play beyond the generation of diversity, including the regulation of stem cell proliferation, the timing of neural stem cell lineage termination, and the coupling of neuronal birth order to circuit assembly.
Patients With Stricturing or Penetrating Crohn’s Disease Phenotypes Report High Disease Burden and Treatment Needs
Authors: Fan Yanni , Zhang Ling , Omidakhsh Negar , Bohn Rhonda L , Thompson Jennifer S , Brodovicz Kimberly G , Deepak Parakkal 
Published: July 2022

Abstract

Background
Crohn’s disease (CD) is a chronic autoimmune disease in which inflammation can progress to complications of stricturing and/or penetrating disease. Real-world data on burden of complicated CD phenotypes are limited.

Methods
We analyzed cross-sectional data from the SPARC IBD (Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease) registry from 2016 to 2020. Four mutually exclusive phenotype cohorts were created: inflammatory CD (CD-I), complicated CD (stricturing CD, penetrating CD, and stricturing and penetrating CD [CD-SP]). Statistical analyses were performed using CD-I as the reference.

Results
A total of 1557 patients were identified: CD-I (n = 674, 43.3%), stricturing CD (n = 457, 29.4%), penetrating CD (n = 166, 10.7%), and CD-SP (n = 260, 16.7%). Patients with complicated phenotypes reported significantly greater use of tumor necrosis factor inhibitors (84.2%-86.7% vs 66.0%; P &lt; .001) and corticosteroids (75.3%-82.7% vs 68.0%; P &lt; .001). Patients with CD-SP reported significantly more aphthous ulcer (15.4% vs 10.5%; P &lt; .05), erythema nodosum (6.5% vs 3.6%; P &lt; .05), inflammatory bowel disease-related arthropathy (25.8% vs 17.2%; P &lt; .01), liquid stools (24.2% vs 9.3%; P &lt; .001), nocturnal fecal incontinence (10.8% vs 2.5%; P &lt; .001), and CD-related surgery (77.7% vs 12.2%; P &lt; .001).

Conclusions
Patients with complicated CD phenotypes reported higher rates of active CD-related luminal and extraintestinal manifestations, and underwent more surgeries, despite being more likely to have received biologics than those with CD-I. The potential for early recognition and management of CD-I to prevent progression to complicated phenotypes should be explored in longitudinal studies.
Den-Associated Behavior ofOctopus rubescensRevealed by a Motion-Activated Camera Trap System
Authors: Humbert Jefferson W , Williams Kresimir , Onthank Kirt L 
Published: July 2022

SynopsisDens are a crucial component of the life history of most shallow water octopuses. However, den usage dynamics have only been explored in a few species over relatively short durations, and Octopus rubescens denning behavior has never been explored in situ. We built four underwater camera traps to observe the behavior of O. rubescens in and around their dens. To distinguish individuals, octopuses were captured and given a unique identifiable visible implant elastomer tag on the dorsal side of their mantle. After being tagged and photographed, each octopus was released back to its original capture site within its original den bottle. The site is unique in that octopuses reside almost exclusively in discarded bottles, therefore aiding in locating and monitoring dens. Motion-activated cameras were suspended in a metal field-of-view above bottle dens of released octopuses to observe den-associated behaviors. Cameras were regularly retrieved and replaced to allow continuous monitoring of den locations in 71 h intervals for over a month. We found that O. rubescenswas primarily active during the day and had frequent interactions with conspecifics (other members within the species). We also found that rockfish and red rock crabs tended to frequent den locations more often when octopuses were not present, while kelp greenling both visited dens more frequently and stayed longer when octopuses were present. Our results, demonstrate the utility of motion-activated camera traps for behavioral and ecological studies of nearshore mobile organisms.
Redesigning patient flow in orthopedics and radiology clinics via a three-phase ‘Kaizen’ improvement approach and interrupted time series analysis
Authors: Sullivan Kali , Topper Langley , Rajwani Aliysa 
Published: July 2022

Abstract

Introduction
The orthopedics clinic at an academic medical center has low patient satisfaction rates for patients that require an X-ray and have difficulty ambulating. The project aimed to reduce the ‘non-value-added’ time during appointments by using Lean and Six Sigma methodologies and enhance patient experience.

Methods
An analysis of the current state was conducted using Gemba walks, interviews with subject matter experts and an interrupted time study to assess baseline data. The project was implemented using a three-phase Kaizen event approach.

Results
Interventions implemented included: (i) re-engineering patient flow and (ii) standardizing appointment scheduling guidelines. The ‘non-value-added’ appointment time was measured post-intervention and it decreased from 17 to 8 min (51%), and 87% (N = 47) of patients rated the scheduling process positively.

Conclusion
Lean, Six Sigma and Kaizen improvement methodologies are invaluable tools to improve operational efficiency. The implemented interventions enhanced patient experience and improved clinic efficiency.
The Mate Screening Motive: How Women Use Luxury Consumption to Signal to Men
Authors: Chen Qihui , Wang Yajin , Ordabayeva Nailya 
Published: July 2022

Abstract
Previous research has found that for men, activating a mating motive increases luxury consumption as a way to attract a romantic partner. However, little is known about the role of luxury consumption in women’s romantic endeavors. The present research conceptualizes a mate screening motive, which explains how women use luxury consumption to romantically signal to men. Six studies and two follow-ups conducted in controlled and field settings show that the mate screening motive boosts women’s consumption of luxury goods as a way to signal their mating standards to men and thereby deter undesirable pursuers. The effect is diminished when mate screening is less necessary such as when external screening tools are available (e.g., screening filters on dating websites), the quality of potential mates is high, and the focus is on selecting a desirable partner rather than deterring undesirable pursuers. The findings have important implications for understanding how consumers use products and brands in romantic relationships and for designing marketing strategies and communication for luxury brands, commercial dating services, and dating apps. Our findings also provide insights for consumers on how to use brands and products as effective communication devices in romantic endeavors.
Environmental Constitutionalism and Duties of Individuals in India
Authors: Bhullar Lovleen 
Published: July 2022

Abstract
Environmental constitutionalism encompasses rights as well as duties of the State and individuals. However, environmental duties of individuals are seldom discussed in detail. What is their contribution to environmental constitutionalism? This article examines the origin and design, as well as judicial adjudication of the fundamental environmental duty of citizens in the Constitution of India to answer this question. It finds that internal and external factors influence the constitutional origin and design of this duty. The constitution drafters viewed this duty as distinct from the duties of the State. However, judicial practice concerning the nature, scope and content of the duty, as well as its implementation and enforcement evidences a dynamic and symbiotic relationship between constitutional environmental rights and duties. The right-holders corresponding to the duty of citizens may include the environment and future generations. These findings provide a framework for the examination of individual environmental duties in other constitutions.
Genuine paracomplete logics
Authors: Borja Macías Verónica , Coniglio Marcelo E , Hernández-Tello Alejandro 
Published: July 2022

Abstract
In 2016, Béziau introduces a restricted notion of paraconsistency, the so-called genuine paraconsistency. A logic is genuine paraconsistent if it rejects the laws $\varphi ,\neg \varphi \vdash \psi $ and $\vdash \neg (\varphi \land \neg \varphi )$. In that paper, the author analyzes, among the three-valued logics, which of them satisfy this property. If we consider multiple-conclusion consequence relations, the dual properties of those above-mentioned are $ \vdash \varphi , \neg \varphi $ and $\neg (\psi \vee \neg \psi ) \vdash $. We call genuine paracomplete logics those rejecting the mentioned properties. We present here an analysis of the three-valued genuine paracomplete logics. A very natural twist structures semantics for these logics is also found in a systematic way. This semantics produces automatically a simple and elegant Hilbert-style characterization for all these logics. Finally, we introduce the logic LGP which is genuine paracomplete is not genuine paraconsistent, not even paraconsistent and cannot be characterized by a single finite logical matrix.
Expanding the genetic engineering toolbox for the metabolically flexible acetogen Eubacterium limosum
Authors: Sanford Patrick A , Woolston Benjamin M 
Published: July 2022

Abstract
Acetogenic bacteria are an increasingly popular choice for producing fuels and chemicals from single carbon (C1) substrates. Eubacterium limosum is a promising acetogen with several native advantages, including the ability to catabolize a wide repertoire of C1 feedstocks and the ability to grow well on agar plates. However, despite its promise as a strain for synthetic biology and metabolic engineering, there are insufficient engineering tools and molecular biology knowledge to leverage its native strengths for these applications. To capitalize on the natural advantages of this organism, here we extended its limited engineering toolbox. We evaluated the copy number of three common plasmid origins of replication and devised a method of controlling copy number and heterologous gene expression level by modulating antibiotic concentration. We further quantitatively assessed the strength and regulatory tightness of a panel of promoters, developing a series of well-characterized vectors for gene expression at varying levels. In addition, we developed a black/white colorimetric genetic reporter assay and leveraged the high oxygen tolerance of E. limosum to develop a simple and rapid transformation protocol that enables benchtop transformation. Finally, we developed two new antibiotic selection markers—doubling the number available for this organism. These developments will enable enhanced metabolic engineering and synthetic biology work with E. limosum.