bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unsupervised construction of gene regulatory network based on single-cell multi-omics data of colorectal cancer
Authors: Cui Lingyu , Li Hongfei , Bian Jilong , Wang Guohua , Liang Yingjian 
Published: February 2023

AbstractIdentifying gene regulatory networks (GRNs) at the resolution of single cells has long been a great challenge, and the advent of single-cell multi-omics data provides unprecedented opportunities to construct GRNs. Here, we propose a novel strategy to integrate omics datasets of single-cell ribonucleic acid sequencing and single-cell Assay for Transposase-Accessible Chromatin using sequencing, and using an unsupervised learning neural network to divide the samples with high copy number variation scores, which are used to infer the GRN in each gene block. Accuracy validation of proposed strategy shows that approximately 80% of transcription factors are directly associated with cancer, colorectal cancer, malignancy and disease by TRRUST; and most transcription factors are prone to produce multiple transcript variants and lead to tumorigenesis by RegNetwork database, respectively. The source code access are available at: https://github.com/Cuily-v/Colorectal_cancer.
Neuropsychiatric disorders following SARS-CoV-2 infection
Authors: Harrison Paul J , Taquet Maxime 
Published: February 2023

Abstract
Several large-scale electronic health records studies have reported increased diagnostic rates for neuropsychiatric disorders following Coronavirus disease 2019 [COVID-19 or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 infection)], but many questions remain. To highlight the issues, we selectively review this literature, focusing on mood disorder, anxiety disorder, psychotic disorder, and cognitive impairment (‘brain fog’). Eight key questions are addressed, comprising: (i) the nature and magnitude of the risks; (ii) their association with severity of infection; (iii) their duration; (iv) whether the risks differ between adults and children, or between men and women; (v) whether prior vaccination protects against them; (vi) the risk profile associated with different SARS-CoV-2 strains; (vii) what the underlying mechanisms might be; and (viii) whether the sequelae can be predicted. We consider the major unknowns, the limitations of electronic health records for research in this area, and the use of additional approaches to help characterize and understand the neuropsychiatric burden of COVID-19.
Interictal discharges in the human brain are travelling waves arising from an epileptogenic source
Authors: Diamond Joshua M , Withers C Price , Chapeton Julio I , Rahman Shareena , Inati Sara K , Zaghloul Kareem A 
Published: February 2023

Abstract
While seizure activity may be electrographically widespread, increasing evidence has suggested that ictal discharges may in fact represent travelling waves propagated from a focal seizure source. Interictal epileptiform discharges (IEDs) are an electrographic manifestation of excessive hypersynchronization of cortical activity that occur between seizures and are considered a marker of potentially epileptogenic tissue. The precise relationship between brain regions demonstrating IEDs and those involved in seizure onset, however, remains poorly understood. Here, we hypothesize that IEDs likewise reflect the receipt of travelling waves propagated from the same regions which give rise to seizures.
Forty patients from our institution who underwent invasive monitoring for epilepsy, proceeded to surgery and had at least one year of follow-up were included in our study. Interictal epileptiform discharges were detected using custom software, validated by a clinical epileptologist.
We show that IEDs reach electrodes in sequences with a consistent temporal ordering, and this ordering matches the timing of receipt of ictal discharges, suggesting that both types of discharges spread as travelling waves. We use a novel approach for localization of ictal discharges, in which time differences of discharge receipt at nearby electrodes are used to compute source location; similar algorithms have been used in acoustics and geophysics. We find that interictal discharges co-localize with ictal discharges. Moreover, interictal discharges tend to localize to the resection territory in patients with good surgical outcome and outside of the resection territory in patients with poor outcome. The seizure source may originate at, and also travel to, spatially distinct IED foci.
Our data provide evidence that interictal discharges may represent travelling waves of pathological activity that are similar to their ictal counterparts, and that both ictal and interictal discharges emerge from common epileptogenic brain regions. Our findings have important clinical implications, as they suggest that seizure source localizations may be derived from interictal discharges, which are much more frequent than seizures.
Tilavonemab in early Alzheimer’s disease: results from a phase 2, randomized, double-blind study
Authors: Florian Hana , Wang Deli , Arnold Steven E , Boada Mercè , Guo Qi , Jin Ziyi , Zheng Hui , Fisseha Nahome , Kalluri Hari Varun , Rendenbach-Mueller Beatrice , Budur Kumar , Gold Michael 
Published: February 2023

Abstract
Tau accumulation in patients with Alzheimer’s disease tracks closely with cognitive decline and plays a role in the later stages of disease progression. This phase 2 study evaluated the safety and efficacy of tilavonemab, an anti-tau monoclonal antibody, in patients with early Alzheimer’s disease.
In this 96-week, randomized, double-blind, placebo-controlled study (NCT02880956), patients aged 55–85 years meeting clinical criteria for early Alzheimer’s disease with a Clinical Dementia Rating-Global Score of 0.5, a Mini-Mental State Examination score of 22 to 30, a Repeatable Battery for the Assessment of Neuropsychological Status-Delayed Memory Index score of ≤85, and a positive amyloid PET scan were randomized 1:1:1:1 to receive one of three doses of tilavonemab (300 mg, 1000 mg, or 2000 mg) or placebo via intravenous infusion every 4 weeks. The primary end point was the change from baseline up to Week 96 in the Clinical Dementia Rating-Sum of Boxes (CDR-SB) score. Safety evaluations included adverse event monitoring and MRI assessments.
A total of 453 patients were randomized, of whom 337 were treated with tilavonemab (300 mg, n = 108; 1000 mg, n = 116; 2000 mg, n = 113) and 116 received placebo. Baseline demographics and disease characteristics were comparable across groups. The mean age was 71.3 (SD 7.0) years, 51.7% were female, and 96.5% were White. At baseline, the mean CDR-SB score was 3.0 (1.2), which worsened through Week 96 for all treatment groups. The least squares mean change from baseline at Week 96 in the CDR-SB score with tilavonemab was not significantly different compared with placebo [300 mg (n = 85): −0.07 (95% confidence interval, CI: −0.83 to 0.69); 1000 mg (n = 91): −0.06 (95% CI: −0.81 to 0.68); 2000 mg (n = 81): 0.16 (95% CI: −0.60 to 0.93); all P ≥ 0.05]. The incidence of any adverse event and MRI findings were generally comparable across groups.
Tilavonemab was generally well tolerated but did not demonstrate efficacy in treating patients with early Alzheimer’s disease. Further investigations of tilavonemab in early Alzheimer’s disease are not warranted.
Return to Travel in the Coronavirus Disease 2019 Pandemic Recovery Period and Implications for Imported Malaria: Reinforcing Prevention, Early Diagnosis, and Appropriate Treatment of Malaria
Authors: Schultz Jonathan S , Mace Kimberly E , Tan Kathrine R 
Published: February 2023

AbstractReturn to international travel in the COVID-19 pandemic recovery period is expected to increase the number of patients with imported malaria in the United States (US). Malaria prevention in travelers and preparedness for timely diagnosis and appropriate treatment are key to minimize imported malaria morbidity and mortality. Intravenous artesunate (IVAS) is now available from commercial distributors in the US for the treatment of severe malaria. Hospitals and pharmacists should have a plan for malaria treatment, including stocking artemether-lumefantrine for uncomplicated malaria, and stocking or planning for rapid procurement of IVAS for the treatment of severe malaria.
Dispositional Balancing and Hegemonic Order: US Response to China’s Financial Statecraft
Authors: Rodrigues Vieira Vinícius G , Vadlamannati Krishna Chaitanya , Li Yuanxin 
Published: February 2023

Abstract
How does the USA react to Chinese initiatives that gather allies from among the states that have been instrumental in sustaining the American-led liberal international order? We contend that Washington deploys dispositional balancing against Beijing, supporting this argument through a close scrutiny of US support for the projects of international developmental organisations (IDOs), such as multilateral development banks (MDBs), that target borrowing members of the Asian Infrastructure Investment Bank (AIIB). In theoretical terms, dispositional balancing is a relatively cheap strategy whereby the hegemon (the USA) reacts to the emerging power (China) by signalling to both old and potential allies its immutable ability to match that rival’s benefits and hence retain its status and order. We build our theory through logit and linear models, tackling potential endogeneity through use of an instrumental variable strategy. In line with the theoretical expectations, we identify that the USA favours AIIB members, particularly those that also display high levels of dependency on Chinese aid, in IDOs/MDBs, wherein Beijing competes with traditional Western donors from the Organisation for Economic Cooperation and Development’s Development Assistance Committee. Our findings contribute to both the debates on hegemonic-order transitions and the growing scholarship on soft balancing, contested multilateralism, and collective financial statecraft.
Multi-item Measures for Paediatric Inflammatory Bowel Diseases: The ABCs of All Those Acronyms
Authors: Ledder Oren , Turner Dan 
Published: February 2023

AbstractWith the recent acceptance of multiple treatment goals for inflammatory bowel diseases [IBD], it becomes increasingly important to accurately quantify the measurable concepts. These include patient-reported symptoms, intestinal damage, mucosal activity, transmural inflammation, and histologicl appearance, as well as quality of life, disability, and other patient-centred attributes. Standardised indices which show sufficient validity, reliability, and responsiveness to change are not only mandatory for implementing the treat to target approach but are also critical for assessing the effectiveness of emerging medications in clinical trial settings. Some concepts can be accurately assessed through the use of existing measurement tools used for adults [eg, capsule endoscopy, ultrasonic, endoscopic, and histological scoring] and others may be age specific. Although several paediatric indices and scales are well established (eg, IMPACT questionnaire, Paediatric Crohn’s Disease Activity Index [PCDAI], and Paediatric Ulcerative Colitis Activity Index [PUCAI]), recent years have seen the development of newer indices for children, including the Mucosal Inflammation Noninvasive Index [MINI] to predict endoscopic healing in Crohn’s disease, magnetic resonance imaging [MRI] indices that measure inflammation (ie, the Paediatric Inflammatory Crohn’s Magnetic Resonance Enterography Index [PICMI]) and perianal disease (ie, Paediatric MRI-based Perianal Crohn’s Disease [PEMPAC]), and patient-reported outcome measures in ulcerative colitis [ie, TUMMY-UC], upper gastrointestinal inflammatory score [ie, UGI-SES-CD], simplified endoscopic mucosal assessment score for Crohn’s disease [SEMA-CD], and the parent-completed IMPACT questionnaire [ie, IMPACT-III-P]. Despite these advances, quantifiable paediatric IBD-specific tools are still lacking for disability and fatigue. In this review, we provide a contemporary, clinically focused overview of the indices that a paediatric gastroenterologist can use to quantify disease status.
Partially reversible lung consolidation after revascularization of a total occlusion of both left pulmonary veins following ablation of atrial fibrillation: a case report
Authors: Ahero Anete , Frauenfelder Thomas , Breitenstein Alexander , Ammann Peter , Kucher Nils , Barco Stefano 
Published: February 2023

AbstractBackgroundThe use of pulmonary vein (PV) radiofrequency ablation for atrial fibrillation (AF) treatment may be complicated by PV stenosis or occlusion. A common curative treatment for symptomatic patients is a transcatheter intervention, including percutaneous transluminal balloon angioplasty and stent implantation. Stent implantation itself, however, can be complicated by in-stent stenosis.Case summaryA 26-year-old man presented with worsening exertional dyspnoea due to a total occlusion of both left PVs after the isolation of two PVs for AF. Chest computed tomography (CT) showed chest asymmetry and consolidation of the left lung. The patient was treated with balloon angioplasty and stent placement of both left PVs, resulting in improvement of symptoms, walking distance, and increase in lung space volume by 120 mL based on CT-based volumetry. Ten months later, the patient experienced a recurrence of similar symptoms. A high grade in stent restenosis of the upper left PV and moderate in stent restenosis of the lower PV were diagnosed and treated with angioplasty. The patient was discharged from the hospital in good clinical condition 3 days after the intervention.DiscussionNon-specific symptoms of PV stenosis or occlusion, such as shortness of breath, fatigue, flu-like symptoms, reduced physical performance, and haemoptysis delay the diagnosis. If unusual symptoms appear abruptly after PV isolation, a PV stenosis should be considered. In this case, we describe for the first time a partially reversible consolidation of lung parenchyma following the revascularization of both PVs.
Targeted care coordination towards patients with a history of multiple readmissions effectively reduces readmissions
Authors: Wellman Courtney D , Franks Adam M , Stickler Morgan , Rollyson William , Korkmaz Alperen , Christiansen Matthew Q , Petrany Stephen M 
Published: February 2023

Abstract

Background
To decrease hospital readmission rates, clinical practices create a transition of care (TOC) process to assess patients and coordinate care postdischarge. As current evidence suggests lack of universal benefit, this study’s objectives are to determine what patient and process factors associate with hospital readmissions, as well as construct a model to decrease 30-day readmissions.

Methods
Three months of retrospective discharged patient data (n = 123) were analysed for readmission influences including: patient-specific comorbidities, admission-specific diagnoses, and TOC components. A structured intervention of weekly contact, the Care Coordination Cocoon (CCC), was created for multiply readmitted patients (MRPs), defined as ≥2 readmissions. Three months of postintervention data (n = 141) were analysed. Overall readmission rates and patient- and process-specific characteristics were analysed for associations with hospital readmission.

Results
Standard TOC lacked significance. Patient-specific comorbidities of cancer (odds ratio [OR] 6.27; 95% confidence interval [CI] 1.73–22.75) and coronary artery disease (OR 6.71; 95% CI 1.84–24.46), and admission-specific diagnoses within pulmonary system admissions (OR 7.20; 95% CI 1.96–26.41) were associated with readmissions. Post-CCC data demonstrated a 48-h call (OR 0.21; 95% CI 0.09–0.50), answered calls (OR 0.16; CI 0.07–0.38), 14-day scheduled visit (OR 0.20; 95% CI 0.07–0.54), and visit arrival (OR 0.39; 95% CI 0.17–0.91) independently associated with decreased readmission rate. Patient-specific (hypertension—OR 3.65; CI 1.03–12.87) and admission-specific (nephrologic system—OR 3.22; CI 1.02–10.14) factors associated with readmissions which differed from the initial analysis.

Conclusions
Targeting a practice’s MRPs with CCC resources improves the association of TOC components with readmissions and rates decreased. This is a more efficient use of TOC resources.
Bottlenecks can constrain and channel evolutionary paths
Authors: Gamblin Jasmine , Gandon Sylvain , Blanquart François , Lambert Amaury 
Published: February 2023

Abstract
Population bottlenecks are commonplace in experimental evolution, specifically in serial passaging experiments where microbial populations alternate between growth and dilution. Natural populations also experience such fluctuations caused by seasonality, resource limitation, or host-to-host transmission for pathogens. Yet, how unlimited growth with periodic bottlenecks influence the adaptation of populations is not fully understood. Here, we study theoretically the effects of bottlenecks on the accessibility of evolutionary paths and on the rate of evolution. We model an asexual population evolving on a minimal fitness landscape consisting of two types of beneficial mutations with the empirically supported trade-off between mutation rate and fitness advantage, in the regime where multiple beneficial mutations may segregate simultaneously. In the limit of large population sizes and small mutation rates, we show the existence of a unique most likely evolutionary scenario, determined by the size of the wild-type population at the beginning and at the end of each cycle. These two key demographic parameters determine which adaptive paths may be taken by the evolving population by controlling the supply of mutants during growth and the loss of mutants at the bottleneck. We do not only show that bottlenecks act as a deterministic control of evolutionary paths but also that each possible evolutionary scenario can be forced to occur by tuning demographic parameters. This work unveils the effects of demography on adaptation of periodically bottlenecked populations and can guide the design of evolution experiments.
Meaningful Work: Cultural Frameworks of Forced Labour in Accounts of Nazi Concentration Camp Inmates
Authors: Falldorf Ella , Kabalek Kobi 
Published: February 2023

Abstract
Studies of forced labour in Nazi camps tend to stress the exceptionality of inmates’ experiences and their profound difference from common views of work. Yet examination of the wartime and postwar accounts of inmates and survivors reveals that they often combine features of the camp reality itself with phenomena from other times, places and situations. In this way, written, oral and visual depictions articulate a reality in which concepts and ideologies of work familiar from various cultural settings mix with those of the Nazi camp system, as well as with later experiences and current debates. This article traces three cultural frameworks that inmates and survivors utilized to make sense of forced labour in Nazi camps: war and the military, industrial concepts of productive destruction and destructive production, and Jewish religious culture. In exploring the relationship between the continuity and discontinuity of meaning between these cultural frameworks and the Nazi camps, we analyse a wide range of interviews, artworks, songs, memoirs and written reports from the 1930s to the early 2000s. We argue that in order not to make their suffering and work appear senseless, inmates and survivors understood forced labour within well-established frameworks of meaning. Their accounts, we suggest, use symbolic elements as creative acts that address inmates’ experiences by expanding the camp reality or going beyond it, thereby making them more comprehensible and communicable.
Excitation of high-latitude MAC waves in Earth’s core
Authors: Nicolas Quentin , Buffett Bruce 
Published: February 2023

SUMMARY
Recent geomagnetic observations reveal localized oscillations in the field’s secular acceleration at high latitudes, with periods of about 20 yr. Several types of waves in rotating magnetized fluids have been proposed to explain equatorial oscillations with similar high frequencies. Among these are non-axisymmetric Alfvén waves, magneto-Coriolis waves and, in the presence of fluid stratification, magnetic-Archimedes–Coriolis (MAC) waves. We explore the hypothesis that the observed high latitude patterns are the signature of MAC waves by modelling their generation in Earth’s core. We quantitatively assess several generation mechanisms using output from dynamo simulations in a theoretical framework due to Lighthill. While the spatio-temporal structure of the sources from the dynamo simulations are expected to be realistic, their amplitudes are extrapolated to reflect differences between the simulation’s parameter space and Earth-like conditions. We estimate full wave spectra spanning monthly to centennial frequencies for three plausible excitation sources: thermal fluctuations, Lorentz force and magnetic induction. When focusing on decadal frequencies, the Lorentz force appears to be most effective in generating high-latitude MAC waves with amplitude estimates falling within an order of magnitude of observed oscillations. Overall, this study puts forward MAC waves as a viable explanation, in the presence of fluid stratification at the top of Earth’s core, for observed field variations at high latitudes.
Homogenization results for the generator of multiscale Langevin dynamics in weighted Sobolev spaces
Authors: Zanoni Andrea 
Published: February 2023

AbstractWe study the homogenization of the Poisson equation with a reaction term and of the eigenvalue problem associated to the generator of multiscale Langevin dynamics. Our analysis extends the theory of two-scale convergence to the case of weighted Sobolev spaces in unbounded domains. We provide convergence results for the solution of the multiscale problems above to their homogenized surrogate. A series of numerical examples corroborate our analysis.
Changes in the Incidence of Invasive Bacterial Disease During the COVID-19 Pandemic in the United States, 2014–2020
Authors: Prasad Namrata , Rhodes Julia , Deng Li , McCarthy Natalie L , Moline Heidi L , Baggs James , Reddy Sujan C , Jernigan John A , Havers Fiona P , Sosin Daniel M , Thomas Ann , Lynfield Ruth , Schaffner William , Reingold Arthur , Burzlaff Kari , Harrison Lee H , Petit Susan , Farley Monica M , Herlihy Rachel , Nanduri Srinivas , Pilishvili Tamara , McNamara Lucy A , Schrag Stephanie J , Fleming-Dutra Katherine E , Kobayashi Miwako , Arvay Melissa 
Published: February 2023

AbstractBackgroundDescriptions of changes in invasive bacterial disease (IBD) epidemiology during the coronavirus disease 2019 (COVID-19) pandemic in the United States are limited.MethodsWe investigated changes in the incidence of IBD due to Streptococcus pneumoniae, Haemophilus influenzae, group A Streptococcus (GAS), and group B Streptococcus (GBS). We defined the COVID-19 pandemic period as 1 March to 31 December 2020. We compared observed IBD incidences during the pandemic to expected incidences, consistent with January 2014 to February 2020 trends. We conducted secondary analysis of a health care database to assess changes in testing by blood and cerebrospinal fluid (CSF) culture during the pandemic.ResultsCompared with expected incidences, the observed incidences of IBD due to S. pneumoniae, H. influenzae, GAS, and GBS were 58%, 60%, 28%, and 12% lower during the pandemic period of 2020, respectively. Declines from expected incidences corresponded closely with implementation of COVID-19–associated nonpharmaceutical interventions (NPIs). Significant declines were observed across all age and race groups, and surveillance sites for S. pneumoniae and H. influenzae. Blood and CSF culture testing rates during the pandemic were comparable to previous years.ConclusionsNPIs likely contributed to the decline in IBD incidence in the United States in 2020; observed declines were unlikely to be driven by reductions in testing.