bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulating groundstate and dynamical quantum phase transitions on a superconducting quantum computer
Authors: Dborin James , Wimalaweera Vinul , Barratt F. , Ostby Eric , O’Brien Thomas E. , Green A. G. 
Published: October 2022

AbstractThe phenomena of quantum criticality underlie many novel collective phenomena found in condensed matter systems. They present a challenge for classical and quantum simulation, in part because of diverging correlation lengths and consequently strong finite-size effects. Tensor network techniques that work directly in the thermodynamic limit can negotiate some of these difficulties. Here, we optimise a translationally invariant, sequential quantum circuit on a superconducting quantum device to simulate the groundstate of the quantum Ising model through its quantum critical point. We further demonstrate how the dynamical quantum critical point found in quenches of this model across its quantum critical point can be simulated. Our approach avoids finite-size scaling effects by using sequential quantum circuits inspired by infinite matrix product states. We provide efficient circuits and a variety of error mitigation strategies to implement, optimise and time-evolve these states.
Unique thermal sensitivity imposes a cold-water energetic barrier for vertical migrators
Authors: Seibel Brad A. , Birk Matthew A. 
Published: October 2022

AbstractAlterations of marine species’ ranges with climate change are often attributed to oxygen limitation in warming oceans. Here we report unique metabolic temperature sensitivities for the myriad of vertically migrating oceanic species that daily cross depth-related gradients in temperature and oxygen. In these taxa, selection favours high metabolic activity for predator–prey interactions in warm shallow water and hypoxia tolerance in the cold at depth. These diverging selective pressures result in thermal insensitivity of oxygen supply capacity and enhanced thermal sensitivity of active metabolic rate. Aerobic scope is diminished in the cold, well beyond thermodynamic influences and regardless of ambient oxygen levels, explaining the native distributions of tropical migrators and their recent range expansions following warming events. Cold waters currently constitute an energetic barrier to latitudinal range expansion in vertical migrators. As warming due to climate change approaches, and eventually surpasses, temperatures seen during past warming events, this energetic barrier will be relieved.
Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome
Authors: Durrant Matthew G. , Fanton Alison , Tycko Josh , Hinks Michaela , Chandrasekaran Sita S. , Perry Nicholas T. , Schaepe Julia , Du Peter P. , Lotfy Peter , Bassik Michael C. , Bintu Lacramioara , Bhatt Ami S. , Hsu Patrick D. 
Published: October 2022

AbstractLarge serine recombinases (LSRs) are DNA integrases that facilitate the site-specific integration of mobile genetic elements into bacterial genomes. Only a few LSRs, such as Bxb1 and PhiC31, have been characterized to date, with limited efficiency as tools for DNA integration in human cells. In this study, we developed a computational approach to identify thousands of LSRs and their DNA attachment sites, expanding known LSR diversity by >100-fold and enabling the prediction of their insertion site specificities. We tested their recombination activity in human cells, classifying them as landing pad, genome-targeting or multi-targeting LSRs. Overall, we achieved up to seven-fold higher recombination than Bxb1 and genome integration efficiencies of 40–75% with cargo sizes over 7 kb. We also demonstrate virus-free, direct integration of plasmid or amplicon libraries for improved functional genomics applications. This systematic discovery of recombinases directly from microbial sequencing data provides a resource of over 60 LSRs experimentally characterized in human cells for large-payload genome insertion without exposed DNA double-stranded breaks.
Effects of elevated systolic blood pressure on ischemic heart disease: a Burden of Proof study
Authors: Razo Christian , Welgan Catherine A. , Johnson Catherine O. , McLaughlin Susan A. , Iannucci Vincent , Rodgers Anthony , Wang Nelson , LeGrand Kate E. , Sorensen Reed J. D. , He Jiawei , Zheng Peng , Aravkin Aleksandr Y. , Hay Simon I. , Murray Christopher J. L. , Roth Gregory A. 
Published: October 2022

AbstractHigh systolic blood pressure (SBP) is a major risk factor for ischemic heart disease (IHD), the leading cause of death worldwide. Using data from published observational studies and controlled trials, we estimated the mean SBP–IHD dose–response function and burden of proof risk function (BPRF), and we calculated a risk outcome score (ROS) and corresponding star rating (one to five). We found a very strong, significant harmful effect of SBP on IHD, with a mean risk—relative to that at 100 mm Hg SBP—of 1.39 (95% uncertainty interval including between-study heterogeneity 1.34–1.44) at 120 mm Hg, 1.81 (1.70–1.93) at 130 mm Hg and 4.48 (3.81–5.26) at 165 mm Hg. The conservative BPRF measure indicated that SBP exposure between 107.5 and 165.0 mm Hg raised risk by 101.36% on average, yielding a ROS of 0.70 and star rating of five. Our analysis shows that IHD risk was already increasing at 120 mm Hg SBP, rising steadily up to 165 mm Hg and increasing less steeply above that point. Our study endorses the need to prioritize and strengthen strategies for screening, to raise awareness of the need for timely diagnosis and treatment of hypertension and to increase the resources allocated for understanding primordial prevention of elevated blood pressure.
Influence of the microbiome, diet and genetics on inter-individual variation in the human plasma metabolome
Authors: Chen Lianmin , Zhernakova Daria V. , Kurilshikov Alexander , Andreu-Sánchez Sergio , Wang Daoming , Augustijn Hannah E. , Vich Vila Arnau ,   Lifelines Cohort Study, Weersma Rinse K. , Medema Marnix H. , Netea Mihai G. , Kuipers Folkert , Wijmenga Cisca , Zhernakova Alexandra , Fu Jingyuan 
Published: October 2022

AbstractThe levels of the thousands of metabolites in the human plasma metabolome are strongly influenced by an individual’s genetics and the composition of their diet and gut microbiome. Here, by assessing 1,183 plasma metabolites in 1,368 extensively phenotyped individuals from the Lifelines DEEP and Genome of the Netherlands cohorts, we quantified the proportion of inter-individual variation in the plasma metabolome explained by different factors, characterizing 610, 85 and 38 metabolites as dominantly associated with diet, the gut microbiome and genetics, respectively. Moreover, a diet quality score derived from metabolite levels was significantly associated with diet quality, as assessed by a detailed food frequency questionnaire. Through Mendelian randomization and mediation analyses, we revealed putative causal relationships between diet, the gut microbiome and metabolites. For example, Mendelian randomization analyses support a potential causal effect ofEubacterium rectalein decreasing plasma levels of hydrogen sulfite—a toxin that affects cardiovascular function. Lastly, based on analysis of the plasma metabolome of 311 individuals at two time points separated by 4 years, we observed a positive correlation between the stability of metabolite levels and the amount of variance in the levels of that metabolite that could be explained in our analysis. Altogether, characterization of factors that explain inter-individual variation in the plasma metabolome can help design approaches for modulating diet or the gut microbiome to shape a healthy metabolome.
Integrated use of regional weather forecasting and crop modeling for water stress assessment on rice yield
Authors: Rajasivaranjan T. , Anandhi Aavudai , Patel N. R. , Irannezhad Masoud , Srinivas C. V. , Veluswamy Kumar , Surendran U. , Raja P. 
Published: October 2022

AbstractThis study evaluated the effects of water stress on rice yield over Punjab and Haryana across North India by integrating Weather Research Forecasting (WRF) and Decision Support System for Agrotechnology Transfer (DSSAT) models. Indian Remote Sensing Satellite datasets were used to define land use/land cover in WRF. The accuracy of simulated rainfall and temperature over Punjab and Haryana was evaluated against Tropical Rainfall Measuring Mission and automated weather station data of Indian Space Research Organization, respectively. Data from WRF was used as weather input to DSSAT to simulate rice yield in Punjab and Haryana for 2009 and 2014. After simulated yield has been evaluated against district-level observed yield, the water balance components within the DSSAT model were used to analyze the impact of water stress on rice yield. The correlation (R2) between the crop water stress factor and the rice yield anomaly at the vegetative and reproductive stage was 0.64 and 0.52 for Haryana and 0.73 and 0.68 for Punjab, respectively. Severe water stress during the flowering to maturity stage inflicted devastating effects on yield. The study concludes that the regional climate simulations can be potentially used for early water stress prediction and its impact on rice yield.
Acute and chronic cardiometabolic responses induced by resistance training with blood flow restriction in HIV patients
Authors: Alves Thiago Cândido , Pugliesi Abdalla Pedro , Bohn Lucimere , Da Silva Leonardo Santos Lopes , dos Santos André Pereira , Tasinafo Júnior Márcio Fernando , Rossini Venturini Ana Cláudia , Mota Jorge , Lopes Machado Dalmo Roberto 
Published: October 2022

AbstractResistance training with blood flow restriction (RTBFR) allows physically impaired people living with HIV (PWH) to exercise at lower intensities than traditional resistance training (TRT). But the acute and chronic cardiac and metabolic responses of PWH following an RTBFR protocol are unknown. The objective was to compare the safety of acute and chronic effects on hemodynamic and lipid profiles between TRT or RTBFR in PWH. In this randomized control trial, 14 PWH were allocated in RTBFR (GRTBFR; n = 7) or TRT (GTRT; n = 7). Both resistance training protocols had 36 sessions (12 weeks, three times per week). Protocol intensity was 30% (GRTBFR) and 80% (GTRT). Hemodynamic (heart rate, blood pressure) and lipid profile were acutely (rest and post exercise 7th, 22nd, and 35th sessions) and chronically (pre and post-program) recorded. General linear models were applied to determine group * time interaction. In the comparisons between groups, the resistance training program showed acute adaptations: hemodynamic responses were not different (p > 0.05), regardless of the assessment session; and chronicles: changes in lipidic profile favors GRTBFR, which significantly lower level of total cholesterol (p = 0.024), triglycerides (p = 0.002) and LDL (p = 0.030) compared to GTRT. RTBFR and TRT induced a similar hemodynamic adaptation in PWH, with no significant risks of increased cardiovascular stress. Additionally, RTBFR promoted better chronic adequacy of lipid profile than TRT. Therefore, RTBFR presents a safe resistance training alternative for PWH.Trial registration: ClinicalTrials.gov ID: NCT02783417; Date of registration: 26/05/2016.
Impact of government policies on the COVID-19 pandemic unraveled by mathematical modelling
Authors: Wilk Agata Małgorzata , Łakomiec Krzysztof , Psiuk-Maksymowicz Krzysztof , Fujarewicz Krzysztof 
Published: October 2022

AbstractSince the very beginning of the COVID-19 pandemic, control policies and restrictions have been the hope for containing the rapid spread of the virus. However, the psychological and economic toll they take on society entails the necessity to develop an optimal control strategy. Assessment of the effectiveness of these interventions aided with mathematical modelling remains a non-trivial issue in terms of numerical conditioning due to the high number of parameters to estimate from a highly noisy dataset and significant correlations between policy timings. We propose a solution to the problem of parameter non-estimability utilizing data from a set of European countries. Treating a subset of parameters as common for all countries and the rest as country-specific, we construct a set of individualized models incorporating 13 different pandemic control measures, and estimate their parameters without prior assumptions. We demonstrate high predictive abilities of these models on an independent validation set and rank the policies by their effectiveness in reducing transmission rates. We show that raising awareness through information campaigns, providing income support, closing schools and workplaces, cancelling public events, and maintaining an open testing policy have the highest potential to mitigate the pandemic.
Clinicopathologic characteristics and prognostic analysis of monoclonal gammopathy of renal significance (MGRS) in patients with IgM monoclonal gammopathy: a case series
Authors: Liu Jing , Liang Dandan , Liang Shaoshan , Xu Feng , Huang Xianghua , Jiang Song , Hou Jinhua 
Published: October 2022

AbstractMonoclonal gammopathy has emerged as an important cause of renal injury. Since the clinicopathologic features related to monotypic monoclonal gammopathy of renal significance with IgM monoclonal gammopathy (IgM-MGRS) are poorly described and it is uncertain if intervention improves renal survival and mortality, we report a series of such patients, characterizing their clinicopathologic spectrum and outcomes. We retrospectively analyzed 38 patients referred to one medical center between 2009 and 2019 with detectable serum monoclonal IgM by immunofixation, performance of a bone marrow biopsy and kidney biopsy-proven MGRS. Of the 38 patients identified, about half patients were amyloidosis, followed by cryoglobulinemic glomerulonephritis. Patients were divided into two groups on the basis of their kidney pathology: amyloid and non-amyloid. Patients with non-amyloidosis were more likely to have renal dysfunction, hematuria, anemia and hypocomplementemia and κ light chain was predominant in this sub-group. Amyloid patients were more often treated with chemotherapy than the non-amyloid patients (P = 0.002). There were no significant differences between amyloid and non-amyloid patients in mortality (48% vs 29%, P = 0.467) and incidence of ESRD (19% vs 59%, P = 0.103). The incidence of ESRD was lower in patients treated with chemotherapy and/or ASCT, compared to those without chemotherapy (25% vs 57%, P = 0.049), and it was also lower in the hematologic responders than non-responders (10% vs 40%, P = 0.047). Our study confirmed a diverse variety of clinicopathological features and outcomes in patients with IgM-MGRS. Chemotherapy and/or ASCT and deep hematologic responses might improve renal prognosis.
Integrated Omics analysis of pig muscle metabolism under the effects of dietary Chlorella vulgaris and exogenous enzymes
Authors: Coelho Diogo , Ribeiro David , Osório Hugo , de Almeida André Martinho , Prates José António Mestre 
Published: October 2022

AbstractMonogastric feeding is dependent on costly conventional feedstuffs. Microalgae such as Chlorella vulgaris are a sustainable alternative; however, its recalcitrant cell wall hinders monogastric digestion. Carbohydrate Active Enzyme (CAZyme) supplementation is a possible solution. The objective of this work was to evaluate the effect of 5% dietary C. vulgaris (CV) and enzymatic supplementation (CV + R—Rovabio® Excel AP; CV + M—four CAZyme mix) on muscle transcriptome and proteome of finishing pigs, in an integrated approach. Control pigs increased the abundance of contractile apparatus (MYH1, MYH2, MYH4) and energy metabolism (CKMT1, NDUFS3) proteins, demonstrating increased nutrient availability. They had increased expression of SCD, characteristic of increased glucose availability, via the activation of SREBP-1c and ChREBP. CV and CV + R pigs upregulated proteolytic and apoptotic genes (BAX, DDA1), whilst increasing the abundance of glucose (UQCRFS1) and fatty acid catabolism (ACADS) proteins. CV + R pigs upregulated ACOT8 and SIRT3 genes as a response to reduced nutrient availability, maintaining energy homeostasis. The cell wall specific CAZyme mix, CV + M, was able to comparatively reduce Omics alterations in the muscle, thereby reducing endogenous nutrient catabolism compared to the CV + R and CV.
Dynamic SARS-CoV-2 emergence algorithm for rationally-designed logical next-generation vaccines
Authors: Maison David P. , Ching Lauren L. , Cleveland Sean B. , Tseng Alanna C. , Nakano Eileen , Shikuma Cecilia M. , Nerurkar Vivek R. 
Published: October 2022

AbstractSARS-CoV-2 worldwide spread and evolution has resulted in variants containing mutations resulting in immune evasive epitopes that decrease vaccine efficacy. We acquired SARS-CoV-2 positive clinical samples and compared the worldwide emerged spike mutations from Variants of Concern/Interest, and developed an algorithm for monitoring the evolution of SARS-CoV-2 in the context of vaccines and monoclonal antibodies. The algorithm partitions logarithmic-transformed prevalence data monthly and Pearson’s correlation determines exponential emergence of amino acid substitutions (AAS) and lineages. The SARS-CoV-2 genome evaluation indicated 49 mutations, with 44 resulting in AAS. Nine of the ten most worldwide prevalent (>70%) spike protein changes have Pearson’s coefficient r > 0.9. The tenth, D614G, has a prevalence >99% and r-value of 0.67. The resulting algorithm is based on the patterns these ten substitutions elucidated. The strong positive correlation of the emerged spike protein changes and algorithmic predictive value can be harnessed in designing vaccines with relevant immunogenic epitopes. Monitoring, next-generation vaccine design, and mAb clinical efficacy must keep up with SARS-CoV-2 evolution, as the virus is predicted to remain endemic.
O-glycosylation and its role in therapeutic proteins
Authors: Thompson Nicole , Wakarchuk Warren 
Published: October 2022

AbstractProtein glycosylation is ubiquitous throughout biology. From bacteria to humans, this post translational modification with sophisticated carbohydrate structures plays a profound role in the interaction of proteins with cells and changes the physiochemical properties of the proteins that carry them. When the glycans are linked to Ser or Thr residues, they are known as O-linked glycans, as the glycosidic linkage is through oxygen. O-glycans are perhaps best known as part of the mucin proteins, however many soluble proteins carry these types of glycans, and that their roles in biology are still being discovered. Many of the soluble proteins that carry O-glycans have a role as therapeutic proteins, and in the 21st century, the application of synthetic biology is starting to be applied to improving these proteins through manipulation of the glycans. This review will explore the role of these O-linked glycans in proteins with pharmaceutical significance, as well as recent advancements in recombinant glycoprotein therapeutics.
Predicting the Outcomes of Internet-Based Cognitive Behavioral Therapy for Tinnitus: Applications of Artificial Neural Network and Support Vector Machine
Authors: Rodrigo Hansapani , Beukes Eldré W. , Andersson Gerhard , Manchaiah Vinaya 
Published: October 2022

Purpose:
Internet-based cognitive behavioral therapy (ICBT) has been found to be effective for tinnitus management, although there is limited understanding about who will benefit the most from ICBT. Traditional statistical models have largely failed to identify the nonlinear associations and hence find strong predictors of success with ICBT. This study aimed at examining the use of an artificial neural network (ANN) and support vector machine (SVM) to identify variables associated with treatment success in ICBT for tinnitus.

Method:
The study involved a secondary analysis of data from 228 individuals who had completed ICBT in previous intervention studies. A 13-point reduction in Tinnitus Functional Index (TFI) was defined as a successful outcome. There were 33 predictor variables, including demographic, tinnitus, hearing-related and treatment-related variables, and clinical factors (anxiety, depression, insomnia, hyperacusis, hearing disability, cognitive function, and life satisfaction). Predictive models using ANN and SVM were developed and evaluated for classification accuracy. SHapley Additive exPlanations (SHAP) analysis was used to identify the relative predictor variable importance using the best predictive model for a successful treatment outcome.

Results:
The best predictive model was achieved with the ANN with an average area under the receiver operating characteristic value of 0.73 ± 0.03. The SHAP analysis revealed that having a higher education level and a greater baseline tinnitus severity were the most critical factors that influence treatment outcome positively.

Conclusions:
Predictive models such as ANN and SVM help predict ICBT treatment outcomes and identify predictors of outcome. However, further work is needed to examine predictors that were not considered in this study as well as to improve the predictive power of these models.

Supplemental Material:

https://doi.org/10.23641/asha.21266487
Dysphagia in the Presence of Varicella-Zoster Virus and SARS-CoV-2: A Case Report on the Role of Speech-Language Pathology
Authors: Wright Margaret , Sleffel Justin 
Published: October 2022

Purpose:
Dysphagia due to cranial nerve neuritis is a rare complication of varicella-zoster virus reactivation. In this case report, we describe a single patient diagnosed with varicella-zoster virus meningitis with acute onset dysphagia, the instrumental assessments and interventions employed by speech-language pathologists (SLPs), and discuss the role of these clinicians in the management of these patients.

Conclusion:
The results of this case study demonstrate the importance of a multidisciplinary team approach and the vital role of SLPs in the evaluation and treatment of dysphagia of unknown etiology.
Prävention der Mutter-zu-Kind-Übertragung des
Hepatitis-B-Virus: Leitlinie zur antiviralen Prophylaxe während der
Schwangerschaft
Authors: Harlfinger Julia , Nußbaumer-Streit Barbara , Gartlehner Gerald 
Published: October 2022

Zusammenfassung
Hintergrund Die meisten Hepatitis-B-Virus-assoziierten Todesfälle
bei Erwachsenen sind die Folge von Infektionen, die diese bereits bei ihrer
Geburt oder in den ersten fünf Lebensjahren erworben haben.
Ziel Die Erweiterung der Leitlinie zur Prävention der
Mutter-zu-Kind-Übertragung des Hepatitis-B-Virus um antivirale
Prophylaxe.
Methode Die Leitlinie wurde von der Weltgesundheitsorganisation (WHO)
gemäß WHO-Standards umgesetzt. Die Zusammenfassung wurde durch
ein Team des WHO Collaborating Centre an der Donau-Universität Krems
(Österreich) auf Deutsch übersetzt.
Ergebnisse Neben der Empfehlung, schwangere Frauen auf das
Hepatitis-B-Virus (HBV) zu testen und Neugeborene so bald wie möglich
nach der Geburt gegen Hepatitis B zu impfen, wurden zwei neue Empfehlungen
formuliert: Schwangere, die positiv auf eine HBV-Infektion getestet werden,
sollen eine Tenofovir-Prophylaxe erhalten. Die WHO empfiehlt in Settings, wo
keine vorgeburtliche HBV-DNA-Bestimmung verfügbar ist, das Testen auf
HBeAg als Alternative. Damit soll die Eignung für eine
Tenofovir-Prophylaxe beurteilt werden.
Editorial
Authors: Simon Steffen , Baumann Freerk 
Published: October 2022

Liebe Leserinnen und Leser,was hat denn Bewegungstherapie mit Palliativmedizin oder Hospizarbeit zu tun? Meinen
die das ernst: Sport im Hospiz? Sollen jetzt selbst Schwerkranke in ihren letzten
Lebenstagen noch aufs Fahrradergometer gesetzt werden? Widersprechen sich hier nicht
die Ansätze und die Ziele?