bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Combination Therapy for Extensively Drug-Resistant Acinetobacter baumannii Necrotizing Pneumonia Complicated by Empyema: A Case Report
Authors: Holger Dana J , Kunz Coyne Ashlan J , Zhao Jing J , Sandhu Avnish , Salimnia Hossein , Rybak Michael J 
Published: March 2022

Abstract
We report our clinical and laboratory experience treating a 50-year-old patient who was critically ill with extensively drug-resistant Acinetobacter baumannii necrotizing pneumonia complicated by empyema in Detroit, Michigan. A precision medicine approach using whole-genome sequencing, susceptibility testing, and synergy analysis guided the selection of rational combination antimicrobial therapy.
Cross-seasonal effects in the American Woodcock: Conditions prior to fall migration relate to migration strategy and implications for conservation
Authors: Graham Clayton L , Steeves Tanner , McWilliams Scott R 
Published: March 2022

AbstractHow postbreeding habitat quality and body composition of migratory birds carry over to influence fall migration strategies and residency merits consideration when creating cross-seasonal conservation plans, especially in breeding populations that are partial migrants. We assessed the influence of postbreeding habitat quality on departure body composition and fall migration patterns in a southern New England breeding population of American Woodcock (Scolopax minor). Woodcock that overwintered near breeding areas (n = 5) had less fat upon capture in fall and used lower quality habitat during the fall than birds that eventually departed on migration (n = 17). Woodcock that departed earlier were long-distance migrants that had inhabited higher quality landscapes prior to migration, departed with less or similar fat stores, stopped over for shorter periods on migration, and arrived earlier on their more southerly wintering areas. In contrast, woodcock that departed later were short-distance migrants that had inhabited lower quality landscapes prior to migration yet stored similar or more fat upon departure, stopped over for longer periods on migration, and arrived relatively late to their more northerly wintering areas. These differences in migration strategies were evident under the same fall environmental conditions and did not appear related to individuals responding to their own condition as would be expected if they were classic condition-based carry-over effects. As such, the southern New England breeding population of woodcock is best categorized as nonfacultative partial migrants (i.e., includes residents, short-distance migrants, and long-distance migrants) that demonstrate weak connectivity between life stages; such populations are excellent for the study of the costs and benefits of migration. The stopover and wintering areas used by woodcock in the coastal mid-Atlantic states deserve conservation and management attention in order to preserve critical habitat throughout their wintering range.
Improving the Measurement of Hostile Sexism
Authors: Archer Allison M N , Clifford Scott 
Published: March 2022

AbstractIn recent years, sexism has played an increasingly pivotal role in American politics, and scholarship examining the importance of gender attitudes for political behavior has surged. Researchers have largely relied on the hostile sexism scale to measure prejudice against women, and this scale seems particularly relevant to political science research. However, this scale measures attitudes with an agree-disagree response format, which has long been recognized as a source of substantial measurement error. In this paper, we introduce a revised version of the hostile sexism scale that instead relies on an item-specific question format. Across three studies, we show that the item-specific scale is strongly related to the agree-disagree scale, but that the item-specific version reduces problems with truncation and tends to improve discriminant and predictive validity. Given these advantages, we conclude by recommending that researchers adopt the item-specific hostile sexism scale.
Humoral response and safety of BNT162b2 mRNA vaccine in children with rheumatic diseases
Authors: Akgün Özlem , Çakmak Figen , Guliyeva Vafa , Demirkan Fatma Gül , Tanatar Ayşe , Hançerli Torun Selda , Çin Dilan , Meşe Sevim , Ağaçfidan Ali , Aktay Ayaz Nuray 
Published: March 2022

Abstract

Objectives
The coronavirus disease 2019 (COVID-19) vaccine represents a cornerstone in tackling the pandemic and with the approval of the BNT162b2 mRNA vaccine in December 2020, it has become a beacon of hope for people around the world, including children. This study aimed to present the data on the humoral response and safety of vaccine in a cohort of patients with paediatric rheumatic diseases receiving immunomodulatory treatments.

Methods
Forty-one children with paediatric rheumatic diseases were included and were vaccinated with the BNT162b2 mRNA vaccine (two doses of 30 µg administered 3–4 weeks apart). To assess the humoral response, IgG antibodies developed against the S1/Receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein at baseline and 3–4 weeks after the second dose were measured. The possible local and systemic side effects and disease activity scores were evaluated during the study period.

Results
After the second dose of vaccine, markedly elevated anti-RBD IgG titres were observed in all patients with a median titre of 20 474 AU/ml [interquartile range (IQR) 6534–36 151] with a good safety profile. The median disease duration was 4.3 (IQR 3.5–5.6) years. In the cohort, 14 (34.1%) received conventional DMARDs (cDMARDs), 16 (39%) received biologic DMARDs (bDMARDs) and 11 (26.8%) received a combined therapy (cDMARDs and bDMARDs). Patients treated with combined therapy [median 4695 (IQR 2764–26 491)] had significantly lower median titres of anti-RBD IgG than those receiving only cDMARDs.

Conclusion
Paediatric rheumatic diseases patients receiving immunomodulatory treatments were able to mount an effective humoral response after two dose regimens of BNT162b2 mRNA vaccine safely without interrupting their current treatments.
A systematic review of live vaccine outcomes in infants exposed to biologic disease modifying anti-rheumatic drugs in utero
Authors: Goulden Bethan , Chua Nicole , Parker Elaine , Giles Ian 
Published: March 2022

Abstract

Objectives
Transplacental passage of certain biologic and targeted synthetic DMARDs leads to detectable levels in the neonate, which may impact on the safety of live vaccines. Guidelines advise delaying live vaccine administration in biologic-exposed infants until they are 7 months old.

Methods
A systematic review of Embase, Medline and Cochrane identified live vaccine outcomes in infants exposed to biologic or targeted synthetic DMARDs in utero.

Results
Studies included 276 in utero exposures to adalimumab, certolizumab, etanercept, infliximab, golimumab, tocilizumab and ustekinumab. Live vaccine exposures at &lt;12 months of age included Bacille Calmette-Guérin (BCG) (n = 215), rotavirus (n = 46), and measles, mumps and rubella (MMR) (n = 12). We identified no reactions following MMR, seven mild reactions to rotavirus vaccination and eight reactions to BCG, including one death. All infants with an adverse reaction to BCG had been exposed to infliximab in utero, and six had received BCG in the first month of life. A freedom of information request to the Medicines and Healthcare products Regulatory Agency revealed four fatal disseminated BCG infections in infants exposed to TNF inhibitors in utero, including infliximab, adalimumab and one unspecified TNF inhibitor.

Conclusion
Most evidence for a clinically harmful effect was for early administration of the BCG vaccine to infants exposed in utero to TNF inhibitors with high transplacental transfer rates.
Increased risk of rheumatoid arthritis in patients with endometriosis: genetic aspects
Authors: Zervou Maria I , Vlachakis Dimitrios , Papageorgiou Louis , Eliopoulos Elias , Goulielmos George N 
Published: March 2022

Abstract
RA is an inflammatory joint disease of an autoimmune nature, with a complex mode of inheritance characterized by chronic and destructive inflammation in the peripheral joints of the hands and feet and irreversible disability. This disorder occurs more often in women, and reproductive and hormonal factors have been shown to be related to increased risk. Endometriosis is a chronic, complex, oestrogen-dependent and progressive gynaecological disorder characterized by the growth of endometrial tissue outside the uterine cavity. Thus far, substantial abnormalities in the immune system of women with endometriosis have been demonstrated. Epidemiological data have suggested a link between endometriosis and the risk of incident RA. The similarities between molecular and cellular pathways of endometriosis and RA may implicate a partially shared genetic background. In this review we present an overview of the shared genetic factors known thus far that are associated with the development of both disorders.
Cluster analysis of upper airway stimulation adherence patterns and implications on clinical care
Authors: Soose Ryan J , Araujo Matheus , Faber Kevin , Roy Asim , Lee Kent , Ni Quan , Srivastava Jaideep , Strollo Patrick J 
Published: March 2022

Abstract

Study Objectives
Upper airway stimulation (UAS) therapy is effective for a subset of obstructive sleep apnea (OSA) patients with continuous positive airway pressure (CPAP) intolerance. While overall adherence is high, some patients have suboptimal adherence, which limits efficacy. Our goal was to identify therapy usage patterns during the first 3 months of therapy to enable targeted strategies for improved adherence.

Methods
Therapy data was retrieved from 2098 patients for three months after device activation. Data included mean and standard deviation (SD) of hours of use, therapy pauses, hours from midnight the therapy was turned ON and OFF, percentage of missing days, and stimulation amplitude. Cluster analysis was performed using Gaussian mixture models that categorized patients into six main groups.

Results
The six groups and their prevalence can be summarized as Cluster 1A: Excellent Use (34%); Cluster 1B: Excellent Use with variable timing (23%); Cluster 2A: Good Use with missing days and late therapy ON (16%), Cluster 2B: Good Use with missing days, late therapy ON, and early therapy OFF (12%); Cluster 3A: Variable Use with frequent missing days (8%); Cluster 3B: Variable Use with frequent pauses (7%). Most patients (85%) are excellent or good users with mean therapy use &gt;6 hours per night.

Conclusions
Cluster analysis of early UAS usage patterns identified six distinct groups that may enable personalized interventions for improved long-term management. Differentiation of the patient clusters may have clinical implications with regard to sleep hygiene education, therapy discomfort, comorbid insomnia, and other conditions that impact adherence.
Metabolic Determinants of Cardiomyocyte Proliferation
Authors: Mohamed Tamer M A , Abouleisa Riham , Hill Bradford G 
Published: March 2022

Abstract
The adult mammalian heart is recalcitrant to regeneration after injury, in part due to the postmitotic nature of cardiomyocytes. Accumulating evidence suggests that cardiomyocyte proliferation in fetal or neonatal mammals and in regenerative non-mammalian models depends on a conducive metabolic state. Results from numerous studies in adult hearts indicate that conditions of relatively low fatty acid oxidation, low reactive oxygen species generation, and high glycolysis are required for induction of cardiomyocyte proliferation. Glycolysis appears particularly important because it provides branchpoint metabolites for several biosynthetic pathways that are essential for synthesis of nucleotides and nucleotide sugars, amino acids, and glycerophospholipids, all of which are required for daughter cell formation. In addition, the proliferative cardiomyocyte phenotype is supported in part by relatively low oxygen tensions and through the actions of critical transcription factors, coactivators, and signaling pathways that promote a more glycolytic and proliferative cardiomyocyte phenotype, such as hypoxia inducible factor 1α (Hif1α), Yes-associated protein (Yap), and ErbB2. Interventions that inhibit glycolysis or its integrated biosynthetic pathways almost universally impair cardiomyocyte proliferative capacity. Furthermore, metabolic enzymes that augment biosynthetic capacity such as phosphoenolpyruvate carboxykinase 2 and pyruvate kinase M2 appear to be amplifiers of cardiomyocyte proliferation. Collectively, these studies suggest that acquisition of a glycolytic and biosynthetic metabolic phenotype is a sine qua non of cardiomyocyte proliferation. Further knowledge of the regulatory mechanisms that control substrate partitioning to coordinate biosynthesis with energy provision could be leveraged to prompt or augment cardiomyocyte division and to promote cardiac repair.
The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia
Authors: Klink Galya V , Safina Ksenia R , Nabieva Elena , Shvyrev Nikita , Garushyants Sofya , Alekseeva Evgeniia , Komissarov Andrey B , Danilenko Daria M , Pochtovyi Andrei A , Divisenko Elizaveta V , Vasilchenko Lyudmila A , Shidlovskaya Elena V , Kuznetsova Nadezhda A ,   The Coronavirus Russian Genetics Initiative (CoRGI) Consortium, Speranskaya Anna S , Samoilov Andrei E , Neverov Alexey D , Popova Anfisa V , Fedonin Gennady G ,   The CRIE Consortium, Akimkin Vasiliy G , Lioznov Dmitry , Gushchin Vladimir A , Shchur Vladimir , Bazykin Georgii A 
Published: March 2022

Abstract
Delta has outcompeted most preexisting variants of SARS-CoV-2, becoming the globally predominant lineage by mid-2021. Its subsequent evolution has led to the emergence of multiple sublineages, most of which are well-mixed between countries. By contrast, here we show that nearly the entire Delta epidemic in Russia has probably descended from a single import event, or from multiple closely timed imports from a single poorly sampled geographic location. Indeed, over 90 per cent of Delta samples in Russia are characterized by the nsp2:K81N + ORF7a:P45L pair of mutations which is rare outside Russia, putting them in the AY.122 sublineage. The AY.122 lineage was frequent in Russia among Delta samples from the start, and has not increased in frequency in other countries where it has been observed, suggesting that its high prevalence in Russia has probably resulted from a random founder effect rather than a transmission advantage. The apartness of the genetic composition of the Delta epidemic in Russia makes Russia somewhat unusual, although not exceptional, among other countries.
Visual Perception of 3D Space and Shape in Time - Part I: 2D Space Perception by 2D Linear Translation
Authors: Afifa Umaima , Carmona Javier , Dinh Amy , Espino Diego , McCarthy Trevor , Ta Brian , Wilson Patrick , Asdell Benjamin , Baik Jinwoo , Biju Archana , Chung Sonia , Dao Christopher , Diamond Mark , Doust Saba , East Angela , Espino Diego , Fleiszig-Evans Kailey , Franco Adrian , Garibay-Gutierrez Anthony , Guha Aparajeeta , Gunturu Roshan , Handley Luke , Honore Christina , Kannan Abinav , Khoo Jared , Khosla Mira , Kittur Chandan , Kwon Alexandra , Lee Jessica , Lwe Nicholas , Mayer Mylan , Mills Elizabeth , Pineda Delilah , Pourebrahim Pasha , Rajacich Jacob , Rizvi Shan , Rosales Liliana , Schummer Leonard , Sefkow Conor , Stangel Alexander , Ta Cindy , Ta Ivy , Tong Natalie , Tsujimoto Kyle , Vu Alyssa , Wang Henry , Yares Amanda , Yamaguchi Natsuko , Yoon Ki Woong , Yu Shuyi , Blaisdell Aaron P. , Arisaka Katsushi 
Published: March 2022

AbstractVisual perception plays a critical role in navigating space and extracting useful semantic information crucial to survival. To identify distant landmarks, we constantly shift gaze vectors through saccades, while still maintaining the visual perception of stable allocentric space. How can we sustain stable allocentric space so effortlessly? To solve this question, we have developed a new concept of NHT (Neural Holography Tomography). This model states that retinotopy is invisible (not available to consciousness) and must be converted to a time code by traveling alpha brainwaves to perceive objects consciously. According to this framework, if identical alpha phases are continually assigned to a landmark, we perceive its exact and consistent allocentric location.To test this hypothesis, we designed reaction time (RT) experiments to observe evidence of the predicted space-to-time conversion. Various visual stimuli were generated at a wide range of eccentricities either on a large TV (up to 40°) or by LED strips on a hemispherical dome (up to 60°). Participants were instructed to report the observed patterns promptly under either covert (no eye movement) or overt (with eye movement) conditions. As predicted, stimuli presented at the center of fixation always produced the fastest RTs. The additional RT delay was precisely proportional to the eccentricity of the peripheral stimulus presentation. Furthermore, both covert and overt attention protocols created the same RT delays, and trajectories of saccadic eye motions were in parallel to the overt RT vs. eccentricity. These findings strongly support our NHT model, in which the observed RT-eccentricity dependence is indicative of the spatiotemporal conversion required for maintaining a stable allocentric frame of reference. That is, we perceive space by time.
Laboratory verification of new commercial lateral flow assays for Cryptococcal antigen (CrAg) detection against the predicate IMMY LFA in a reference laboratory in South Africa
Authors: Coetzee Lindi-Marie , Glencross Deborah Kim 
Published: March 2022

AbstractBackgroundReflex Cryptococcal antigen (CrAg) testing in HIV-positive patients is done routinely at 47 laboratories in South Africa on samples with a confirmed CD4 count <100 cells/μl, using the IMMY Lateral Flow Assay (LFA) as the standardized predicate method.ObjectiveThis study aimed to verify the diagnostic performance of newer CrAg LFA assays against the predicate method.MethodsRemnant CD4 samples collected between February and June 2019, with confirmed predicate LFA CrAg results, were retested on settled plasma with the (i) IMMY CrAg semi-quantitative (SQ) LFA; (ii) Bio-Rad RDT CryptoPS SQ; and (iii) Dynamiker CrAg SQ assays, within 24 hours of predicate testing. Sensitivity/ specificity analyses were conducted comparing predicate versus the newer assays, with McNemar’s test’s p-values reported for comparative results (p values <0.05 significant). Positivity grading was noted for the IMMY SQ and Bio-Rad assays.ResultsOf the 254 samples tested, 228 had comparative CrAg results across all assays. The predicate method reported 85 CrAg positive (37.2%), compared to between 35.08 and 37.28% for the Bio-Rad, IMMY SQ and Dynamiker assays. The IMMY CrAg SQ grading (+1 to +5) showed 67% of CrAg positive results had a grading ≥3, indicative of higher CrAg concentration (infection severity). False-negative results across all assays were <2%, with sensitivity >95% for all. False-positive results were highest for the Dynamiker LFA (14%) with a specificity of 77% (p=0.001). IMMY SQ and Bio-Rad assays specificities exceeded 90% (p=0.6 and 0.12). Internal quality control showed 100% accuracy for all assays.ConclusionPerformance verification of newer CrAg LFA assays under typical laboratory conditions varied, with best results by IMMY SQ and Bio-Rad. The high burden of HIV and cryptococcal disease in South Africa requires high specificity and - sensitivity (>90%) to prevent unnecessary treatment/hospitalization. The added value of positivity grading for patient management needs confirmation.
Molecular mechanisms of long-term light adaptation of an extremophilic alga Cyanidioschyzon merolae
Authors: Abram Mateusz , Kaňa Radek , Olofsson Didrik , Pniewski Filip , Šedivá Barbora , Stark Martha , Fossl Dylan , Slat Viktor , Neumann Alexander , Rader Stephen , Kargul Joanna 
Published: March 2022

AbstractOxygenic phototrophs have evolved a remarkable plethora of strategies to react to changes in light intensity and spectral range, which allows them to thrive in a wide range of environmental conditions. Varying light quality and quantity influences the balance between solar energy capture and utilisation in photosynthesis, affecting concomitantly the downstream processes of central carbon and nitrogen metabolism as well as cellular growth and division. Here, we performed a comprehensive analysis of the mechanisms of long-term photoacclimation of an extremophilic red alga Cyanidioschyzon merolae that grows in sulphuric hot springs at high temperatures and low pH. By using spectroscopic, confocal fluorescence microscopy, photosynthetic performance measurements and global transcriptome analyses, we identified several molecular mechanisms underlying the long-term adaptation of this acido-thermophilic red alga to varying light intensity and spectral quality. These include: (1) remodelling of the functional antenna size of both photosystems; (2) rearrangement of the PSB/PSII/PSI microdomains within thylakoids; (3) modulation of the photosynthetic performance parameters, especially at the level of non-photochemical quenching, and (4) transcriptional regulation of photosynthesis and its regulatory components as well as downstream metabolic pathways related to ROS detoxification, cell/organelle division, and central carbon and nitrogen metabolism. Such an intricate network of interplay between light-driven reactions and downstream metabolic pathways provides the necessary basis for maintaining the highest photosynthetic performance under light-limiting conditions.
Computational Assessment of Different Structural Models for Claudin-5 Complexes in Blood-Brain-Barrier Tight-Junctions
Authors: Berselli Alessandro , Alberini Giulio , Benfenati Fabio , Maragliano Luca 
Published: March 2022

ABSTRACTThe blood-brain barrier (BBB) strictly regulates the exchange of ions and molecules between the blood and the central nervous system. Tight junctions (TJs) are multimeric structures that control the transport through the paracellular spaces between adjacent brain endothelial cells of the BBB. Claudin-5 (Cldn5) proteins are essential for the TJ formation and assemble into multi-protein complexes via cis-interactions within the same cell membrane and trans-interactions across two contiguous cells. Despite the relevant biological function of Cldn5 proteins and their role as targets of brain drug delivery strategies, the molecular details of their assembly within TJs are still unclear. Two different structural models have been recently introduced, in which Cldn5 dimers belonging to opposite cells join to generate paracellular pores. However, a comparison of these models in terms of ionic transport features is still lacking. In this work, we used molecular dynamics simulations and free energy (FE) calculations to assess the two Cldn5 pore models and investigate the thermodynamic properties of water and physiological ions permeating through them. Despite different FE profiles, both structures present single/multiple FE barriers to ionic permeation, while being permissive to water flux. These results reveal that both models are compatible with the physiological role of Cldn5 TJ strands. By identifying the protein-protein surface at the core of TJ Cldn5 assemblies, our computational investigation provides a basis for the rational design of synthetic peptides and other molecules capable of opening paracellular pores in the BBB.