bluuebunny/crossref_metadata_2025 huggingface dataset:
Resting state hyperconnectivity of the default mode network in schizophrenia and clinical high-risk state for psychosis
Authors: Sasabayashi Daiki , Takahashi Tsutomu , Takayanagi Yoichiro , Nemoto Kiyotaka , Ueno Maya , Furuichi Atsushi , Higuchi Yuko , Mizukami Yuko , Kobayashi Haruko , Yuasa Yusuke , Noguchi Kyo , Suzuki Michio
Published: April 2023

Disrupted functional connectivity (FC) of the default mode network (DMN) may have a pathophysiological role in schizophrenia. However, functional magnetic resonance imaging (fMRI) of the DMN in schizophrenia patients has shown inconsistent results. It also remains unclear whether individuals with at-risk mental state (ARMS) have an altered DMN connectivity and whether it is related to clinical characteristics. This fMRI study examined resting-state FCs of the DMN and its relevance to clinical/cognitive variables in 41 schizophrenia patients, 31 ARMS individuals, and 65 healthy controls. Compared with controls, schizophrenia patients had significantly increased FCs within the DMN and between the DMN and diverse cortical areas, whereas ARMS patients had increased FCs only between the DMN and occipital cortex. FC of the lateral parietal cortex with superior temporal gyrus was positively correlated with negative symptoms in schizophrenia, whereas FC of that with interparietal sulcus was negatively correlated with general cognitive impairment in ARMS. Our findings suggest that increased FCs between the DMN and visual network commonly seen in schizophrenia and ARMS subjects may reflect a network-level disturbance representing a general vulnerability to psychosis. In addition, FC changes related to the lateral parietal cortex may underpin clinical characteristics of ARMS and schizophrenia subjects.
Impact of Hepatitis C Virus Infection and Treatment on Mortality in the Country of Georgia, 2015–2020
Authors: Gvinjilia Lia , Baliashvili Davit , Shadaker Shaun , Averhoff Francisco , Kandelaki Levan , Kereselidze Maia , Tsertsvadze Tengiz , Chkhartishvili Nikoloz , Butsashvili Maia , Metreveli David , Gamkrelidze Amiran , Armstrong Paige A
Published: April 2023

Background

Mortality related to hepatitis C virus (HCV) infection is a key indicator for elimination. We assessed the impact of HCV infection and treatment on mortality in the country of Georgia during 2015–2020.

Methods

We conducted a population-based cohort study using data from Georgia's national HCV Elimination Program and death registry. We calculated all-cause mortality rates in 6 cohorts: (1) Negative for anti-HCV; (2) anti-HCV positive, unknown viremia status; (3) current HCV infection and untreated; (4) discontinued treatment; (5) completed treatment, no sustained virologic response (SVR) assessment; (6) completed treatment and achieved SVR. Cox proportional hazards models were used to calculate adjusted hazards ratios and confidence intervals. We calculated the cause-specific mortality rates attributable to liver-related causes.

Results

After a median follow-up of 743 days, 100 371 (5.7%) of 1 764 324 study participants died. The highest mortality rate was observed among HCV infected patients who discontinued treatment (10.62 deaths per 100 PY, 95% confidence interval [CI]: 9.65, 11.68), and untreated group (10.33 deaths per 100 PY, 95% CI: 9.96, 10.71). In adjusted Cox proportional hazards model, the untreated group had almost 6-times higher hazard of death compared to treated groups with or without documented SVR (adjusted hazard ratio [aHR] = 5.56, 95% CI: 4.89, 6.31). Those who achieved SVR had consistently lower liver-related mortality compared to cohorts with current or past exposure to HCV.

Conclusions

This large population-based cohort study demonstrated the marked beneficial association between hepatitis C treatment and mortality. The high mortality rates observed among HCV infected and untreated persons highlights the need to prioritize linkage to care and treatment to achieve elimination goals.
A Randomized, Controlled, Noninferiority, Multicenter Trial of Systemic vs Intralesional Treatment With Meglumine Antimoniate for Cutaneous Leishmaniasis in Brazil
Authors: Lyra Marcelo R , Oliveira Liliane F A , Schubach Armando O , Sampaio Raimunda N R , Rodrigues Bruna C , Hueb Marcia , Cota Gláucia , Silva Rosiana E , Francesconi Fabio , Pompilio Maurício A , França Adriana O , Amato Valdir S , Souza Regina M , Oliveira Raquel V C , Valete Cláudia M , Pimentel Maria I F
Published: April 2023

Background

Meglumine antimoniate (MA) remains the main treatment for cutaneous leishmaniasis (CL). Uncontrolled studies suggest that intralesional MA (IL-MA) may be noninferior and safer than systemic MA (S-MA).

Methods

Multicenter, randomized, controlled, open-label, phase 3 clinical trial to evaluate the efficacy and toxicity of IL-MA in 3 infiltrations at 14-day intervals compared with S-MA (10–20 mg Sb5+/kg/day, 20 days) for CL, with noninferiority margin of 20%. Primary and secondary outcomes were definitive cure at day 180 and epithelialization rate at day 90 of treatment, respectively. A 2-year follow-up was performed to assess relapses and emergence of mucosal lesions. Adverse events (AEs) were monitored according to the Division of AIDS AE grading system.

Results

We evaluated 135 patients. The cure rates (95% confidence interval) for IL-MA and S-MA treatment were, respectively, 82.8% (70.5–91.4) and 67.8% (53.3–78.3) per protocol (PP) and 70.6% (58.3–81.0) and 59.7% (47.0–71.5) per intention to treat (ITT). The epithelialization rates of the IL-MA and S-MA treatment were, respectively, 79.3% (66.6–88 + 8) and 71.2% (57.9–82.2) PP and 69.1% (55.2–78.5) and 64.2% (50.0–74.2) ITT. AEs in the IL-MA and S-MA groups were, respectively, clinical, 45.6% and 80.6%; laboratory, 26.5% and 73.1%; and electrocardiogram, 8.8% and 25.4%. Ten participants in the S-MA group and 1 in the IL-MA group were discontinued due to severe or persistent AEs.

Conclusions

IL-MA provides a similar cure rate and results in less toxicity compared with S-MA and may be used as first-line therapy for CL patients.

Clinical Trials Registration

REBEC: RBR-6mk5n4.
The degree of utilisation and the slow adjustment of capacity to demand: reflections on the US Economy from the perspective of the Sraffian Supermultiplier
Authors: Haluska Guilherme , Summa Ricardo , Serrano Franklin
Published: April 2023

The purpose of this paper is to show that the Sraffian Supermultiplier demand-led growth model with an exogenous normal degree of capacity utilisation can be used to analyse the long-lasting reduction in the average actual degree of capacity utilisation in the US economy since the early 2000s. We follow the concept of normal degree of utilisation proposed by Ciccone and we use a simple version of the Supermultiplier model in which the adjustment of capacity to demand is slow. We show this in two steps. First, we examined the data for the industrial sector for the US economy and found no relevant change in the average-to-peak indicators, which could indicate a general reduction in the normal degree of capacity utilisation. Second, we made two simulations based on our simple Sraffian Supermultiplier model to demonstrate that (i) the process of convergence of actual utilisation to its given normal degree is slow and the model is compatible with long and lasting deviations between actual and normal utilisation after large shocks, and (ii) that successive decreases in output growth rates in the US economy since the begin of the 2000s, combined with a flexible accelerator mechanism, could explain the decrease in average utilisation.
Hormonal variation and temporal dynamics of musth in Asian elephants (Elephas maximus) are associated with age, body condition and the social environment
Authors: LaDue Chase A , Hunt Kathleen E , Kiso Wendy K , Freeman Elizabeth W
Published: April 2023

The sustainability of endangered Asian elephants in human care is threatened in part by low breeding success and concerns over individual animal wellbeing. Male elephants have received less research attention compared to females, yet males deserve special consideration due to their unique reproductive biology (particularly the sexual state of “musth”) and the complex interaction of physiological, environmental, and social pressures they face. We measured fecal androgen metabolites (FAMs), fecal glucocorticoid metabolites (FGMs), and fecal triiodothyronine metabolites (FT3s) collected weekly over approximately 12 months from 26 male Asian elephants housed in zoos across the US, hypothesizing that FAM, FGM, and FT3 concentrations would be associated with temporal correlates of musth and would vary further with intrinsic (musth status, age, body condition) and extrinsic (social environment) factors. The duration of each musth episode was positively associated with exposure to male conspecifics and negatively associated with body condition. Further, elevated FAM concentrations were associated with social exposure, age, and body condition, and FGM concentrations also varied with age and body condition. FT3 concentrations were not associated with any factor we measured. We also identified periods of lower FAM concentration than confirmed musth episodes (but still higher than baseline FAM concentrations) that we termed “elevated FAM episodes.” The durations of these episodes were negatively correlated with exposure to other male elephants. Together, these results provide evidence that hormone profiles (including those that are predicted to change around musth) vary significantly between male Asian elephants in a way that may be attributed to intrinsic and extrinsic factors. Studies like these serve to enhance the sustainability of ex-situ populations by providing wildlife managers with information to enhance the health, welfare, and reproduction of threatened species like Asian elephants.
Management of bleeding in patients on direct oral anticoagulants in emergency department: where we are and where we are going
Authors: De Marco Francesca , Valli Gabriele , Ancona Carlo , Ruggieri Maria Pia
Published: April 2023

Many patients who access in the emergency department for acute bleeding are on anticoagulants; before specific reversal agents were developed, bleeding on anticoagulants was burdened with a substantial increase in morbidity and mortality. Clinical trials demonstrated favourable risk-benefit profiles of direct-acting oral anticoagulants compared with vitamin K antagonists in patients with atrial fibrillation and compared with low molecular weight heparin in patients treated and prevented from venous thromboembolism. Even if they drastically reduced some types of bleeding, particularly intracranial haemorrhage, they have not completely eliminated this risk. The arrival of a patient with active bleeding in the emergency department is always a critical scenario that involves resources and costs. In critical setting, the diagnosis and treatment of bleeding should occurred simultaneously. Understanding the pathophysiological mechanisms that occur during bleeding is essential for establish the most appropriate therapies and improve the standard of care of the haemorrhagic patients.
Calcified coronary lesions
Authors: Cialdella Pio , Sergi Sonia Cristina , Zimbardo Giuseppe , Donahue Michael , Talarico Giovanni Paolo , Lombardi d’Aquino Umberto Maria , Di Fusco Paolo , Calò Leonardo
Published: April 2023

The treatment of calcific coronary lesions is still a major interventional issue in haemodynamics laboratories. The prevalence of the disease is even increasing, considering the general ageing of the population undergoing coronarography, as well as the often associated comorbidities. In recent years, new devices have been developed that allow both better identification and also better treatment of these lesions. The aim of this review is to summarize both imaging modalities and dedicated techniques and materials, thus providing a kind of compendium for the treatment approach.
Diagnostic and prognostic role of late gadolinium enhancement in cardiomyopathies
Authors: Aquaro Giovanni Donato , De Gori Carmelo , Faggioni Lorenzo , Parisella Maria Luisa , Cioni Dania , Lencioni Riccardo , Neri Emanuele
Published: April 2023

Late gadolinium enhancement (LGE) is the most relevant tool of cardiac magnetic resonance for tissue characterization, and it plays a pivotal role for diagnostic and prognostic assessment of cardiomyopathies. The pattern of presentation of LGE allows differential diagnosis between ischaemic and non-ischaemic heart disease with high diagnostic accuracy, and among different cardiomyopathies, specific presentation of LGE may help to make a diagnosis. Late gadolinium enhancement may be caused by conditions that significantly increase the interstitial space or, less frequently, that slow down Gd exit, like myocardial fibrosis. In chronic myocardial infarction, hypertrophic cardiomyopathies (HCM), dilated cardiomyopathy, Fabry disease, and other conditions, LGE is a marker of myocardial fibrosis, but also in patients with acute myocarditis where LGE may be also explained by the increase of interstitial space caused by interstitial oedema or by tissue infiltration of inflammatory cells. In cardiac amyloidosis, LGE represents myocardial fibrosis but the interstitial overload of amyloid proteins should also be considered as a potential cause of LGE. The identification of the pattern of presentation of LGE is also very important. In the ischaemic pattern, LGE always involves the subendocardial layer with more or less transmural extent, it is confluent, and every single scar should be located in the territory of one coronary artery. In the non-ischaemic pattern, LGE does not fulfil the previous criteria, being midwall, subepicardial, or mixed, not necessarily confluent or confined to a territory of one coronary artery. For cardiomyopathies, the exact pattern of non-ischaemic LGE is important. Quantitative analysis of LGE is required in some specific conditions as in HCM. Magnetic resonance imaging with LGE technique should be performed in every patient with suspect of cardiomyopathy. The lack of standardization of pulse sequence and mostly of quantification methods is the main limitation of LGE technique.
Pragmatic electrocardiogram tracings in non-ischaemic dilated cardiomyopathy: diagnostic and prognostic role
Authors: Pezzato Andrea , Milandri Agnese , Tortorici Gianfranco , Sinagra Gianfranco , Merlo Marco
Published: April 2023

Dilated cardiomyopathy (DCM) is a primitive heart muscle disease characterized by a great heterogeneous aetiology and prognostic outcome. Dilated cardiomyopathy is an umbrella term encompassing different aetiologies that might require specific treatments. It principally affects young and male adults, with high-risk arrhythmic competitive risk. Unfortunately, the prevention of major ventricular arrhythmic events remains a clinical challenge. In the era of advanced multimodality imaging and widely available genetic testing, electrocardiogram (ECG) continues to represent a reliable diagnostic tool, for specific work up of every single patient. However, approaching DCM patients, only a cardiomyopathy-oriented reading makes the role of ECG central in the management of DCM, both for diagnosis, prognosis, and therapeutic management. In this paper, we present four ECGs of four different DCM patients, in order to guide a cardiomyopathy-oriented ECG reading, emphasizing its impact in an early, cost-effective, and personalized diagnostic and prognostic work up in this specific setting.
Electrocardiogram in arrhytmogenic cardiomyopathy
Authors: Calò Leonardo , Oliviero Giada , Crescenzi Cinzia , Romeo Fabiana , Martino Annamaria , Bressi Edoardo , Stefanini Matteo , Silvetti Elisa , Danza Ludovica , Rebecchi Marco , Canestrelli Stefano , Fedele Elisa , Lanzillo Chiara , Fusco Armando , De Ruvo Ermenegildo
Published: April 2023

Criteria for diagnosis of arrhythmogenic cardiomyopathy (ACM) were first proposed in 1994 and subsequently revised in 2010 and in 2020 by an international task force. According to the last consensus of 2020, ACM is defined as a heart muscle disease affecting right ventricle, left ventricle or both, whose principal pathologic feature is fibrofatty myocardial replacement that impairs systolic ventricular function and predisposes to lethal ventricular arrhythmias. ECG findings not only could help to early recognize affected patients but also could identify the ones with maximum risk of ventricular arrhythmias and sudden cardiac death.
Management of heart failure: similarities and discrepancies between the European Society of Cardiology and the American Heart Association guidelines
Authors: Parlati Antonio Luca Maria , Basile Christian , Perrone-Filardi Pasquale
Published: April 2023

Recommendations are the fundamental elements of guidelines and are especially significant when the amount of scientific data is expanding fast, as is the scenario of heart failure (HF). Beginning with the four pillars of treatment for HF with reduced ejection fraction, the main messages of the two most recent major HF guidelines, endorsed by the European Society of Cardiology (ESC) and the American College of Cardiology/American Heart Association/Heart Failure Society of America (ACC/AHA/HFSA), partially overlap. There are notable differences, in part due to the timing of recent publications, like the Universal Definition of HF and the EMPEROR-Preserved trial, and in part due to differing perspectives on the natural history of HF. Specific challenges, such as risk stratification and the use of implanted cardioverter-defibrillators for primary prevention in HFrEF patients with non-ischaemic aetiology, are approached from a variety of perspectives. The ACC/AHA/HFSA recommendations place increased attention on topics that are especially pertinent to the US context, such as the cost-effectiveness of medications and the impact of health inequalities on HF care. A comparison of guideline suggestions may assist readers get a better grasp of the ESC and ACC/AHA/HFSA guidelines and apply logical ways to their own practice, wherever in the world that may be. A comparison may also contribute to the harmonization of future guidelines’ recommendations by highlighting the reasons why certain areas have resulted to different recommendations while seemingly analysing the same published information.
Advanced heart failure: from definitions to therapeutic options
Authors: Garascia Andrea , Palazzini Matteo , Tedeschi Andrea , Sacco Alice , Oliva Fabrizio , Gentile Piero
Published: April 2023

Advanced heart failure (AHF) represents an ominous stage of heart failure (HF), where the expected prognosis remains poor regardless of the improvement in medical knowledge. In this review, we summarize the definition, prognosis, physiopathology, and clinical/therapeutic management of the disease, focusing on the fast and timely referral of the patient to the AHF facilities. We provide an insight of the diagnostic and therapeutic ‘work up’ performed in an Italian AHF hub, implying a deep phenotypical patients characterization in order to evaluate candidacy to the therapeutic gold standards as heart transplantation (HTx) and left ventricular assist device (LVAD).
Acute coronary complications in chronic total occlusion interventions
Authors: Leone Pier Pasquale , Calò Leonardo , Donahue Michael , Gasparini Gabriele
Published: April 2023

Chronic total occlusion (CTO) interventions are among the most complex procedures within the panorama of percutaneous coronary intervention (PCI). Awareness of potential complications, adequate procedural planning in order to avoid them, and prompt recognition and management should any occur are at the cornerstone of a successful CTO programme. Complications can be acute or late after the procedure and can be cardiac or non-cardiac. Acute cardiac complications can occur directly at the coronary artery level or can have other strictly non-coronary manifestations, such as hypotension, myocardial infarction, arrhythmias, or tamponade. In this review, we focus on acute coronary complications of CTO PCI, in particular their causes, prevention, and management strategies.
Evolution of interventional imaging in structural heart disease
Authors: Agricola Eustachio , Ingallina Giacomo , Ancona Francesco , Biondi Federico , Margonato Davide , Barki Monica , Tavernese Annamaria , Belli Martina , Stella Stefano
Published: April 2023

Treatments for structural heart diseases (SHD) have been considerably evolved by the widespread of transcatheter approach in the last decades. The progression of transcatheter treatments for SHD was feasible due to the improvement of devices and the advances in imaging techniques. In this setting, the cardiovascular imaging is pivotal not only for the diagnosis but even for the treatment of SHD. With the aim of fulfilling these tasks, a multimodality imaging approach with new imaging tools for pre-procedural planning, intra-procedural guidance, and follow-up of SHD was developed. This review will describe the current state-of-the-art imaging techniques for the most common percutaneous interventions as well as the new imaging tools. The imaging approaches will be addressed describing the use in pre-procedural planning, intra-procedural guidance, and follow-up.
Tissue thickness measured with dielectric-based technology during radiofrequency catheter ablation
Authors: De Ruvo Ermenegildo , De Luca Lucia , Grieco Domenico , Fagagnini Alessandro , Rebecchi Marco , Schillaci Vincenzo , Stabile Giuseppe , Arestia Alberto , Salito Armando , Martino Anna Maria , Calò Leonardo , Solimene Francesco
Published: April 2023

Radiofrequency catheter ablation of the cavotricuspid isthmus is the standard treatment for patients suffering from typical atrial flutter. The aim of this study was to test the feasibility of tissue thickness and lesion transmurality measurement by a novel dielectric system. This was a retrospective multicentric non-randomized open-label, single-arm study. The atrial wall thickness was significantly higher close to the tricuspid annulus than close to the inferior vena cava and a trend towards a progressive decrease of atrial wall thickness was observed moving the mapping catheter from the tricuspid valve to the inferior vena cava. The possibility to visualize the tissue thickness could modify the way to deliver radiofrequency energy, allowing a tailored approach in cardiac ablation procedures.
Sodium-glucose co-transporter 2 inhibitors in heart failure: an updated evidence-based practical guidance for clinicians
Authors: Monzo Luca , Ferrari Ilaria , Cicogna Francesco , Tota Claudia , Cice Gennaro , Girerd Nicolas , Calò Leonardo
Published: April 2023

The sodium-glucose co-transporter 2 (SGLT2) inhibitors have been shown to reduce risks of clinical events in patients with heart failure (HF), with early and sustained benefits regardless of ejection fraction, diabetic status, and care setting. As part and parcel of the modern foundational HF therapy, clinicians should be familiar with these drugs, in order to implement their use and limit the potential adverse effects. We present an up-to-date review of current evidence and a practical guide for the prescription of SGLT2 inhibitors in patients with HF, highlighting important elements for patient selection, treatment initiation, dosing, and problem solving.
Uncovering the role of microRNA671-5p/CDCA7L/monoamine oxidase-A signaling in Helicobacter pylori mediated apoptosis in gastric epithelial cells
Authors: Lepcha Thurbu Tshering , Kumar Manish , Sharma Arun Kumar , Mal Soumya , Majumder Debayan , Jana Kuladip , Basu Joyoti , Kundu Manikuntala
Published: April 2023

Helicobacter pylori is a gram-negative microaerophilic bacterium and is associated with gastrointestinal diseases ranging from peptic ulcer and gastritis to gastric cancer and mucosa-associated lymphoid tissue lymphoma. In our laboratory, the transcriptomes and miRnomes of AGS cells infected with H. pylori have been profiled, and an miRNA–mRNA network has been constructed. MicroRNA 671-5p is upregulated during H. pylori infection of AGS cells or of mice. In this study, the role of miR-671-5p during infection has been investigated. It has been validated that miR-671-5p targets the transcriptional repressor CDCA7L, which is downregulated during infection (in vitro and in vivo) concomitant with miR-671-5p upregulation. Further, it has been established that the expression of monoamine oxidase A (MAO-A) is repressed by CDCA7L, and that MAO-A triggers the generation of reactive oxygen species (ROS). Consequently, miR-671-5p/CDCA7L signaling is linked to the generation of ROS during H. pylori infection. Finally, it has been demonstrated that ROS-mediated caspase 3 activation and apoptosis that occurs during H. pylori infection, is dependent on the miR-671-5p/CDCA7L/MAO-A axis. Based on the above reports, it is suggested that targeting miR-671-5p could offer a means of regulating the course and consequences of H. pylori infection.
Production of single cell oil by two novel nonconventional yeast strains of Curvibasidium sp. isolated from medicinal lichen
Authors: Bai Long , Cheng Cheng , Sun Meng-Lin , Li Jun , Zou Yue , Zhao Quanyu , Zhao Xin-Qing
Published: April 2023

Oleaginous yeasts utilize renewable resources to produce lipids, which benefits sustainable development, and it is of great interest to screen robust lipid producers. Curvibasidium sp. belongs to nonconventional yeast that are very limitedly studied. Here, two cold-adaptive strains of Curvibasidium sp., namely, Y230 and Y231, isolated from the medicinal lichen Usnea diffracta were investigated for their potential in lipid production. Genome mining of Curvibasidium sp. Y231 was performed, and the special features related to fatty acid biosynthesis were revealed. Glucose, xylose, and glycerol were tested as sole carbon sources for yeast cell growth and lipid production. The total lipid contents of Curvibasidium sp. Y230 and Y231 range from 38.43% to 54.62% of the cell dry cell weight at 20°C, and glucose is the optimal carbon source. These results indicate that the Curvibasidium sp. strains are promising for sustainable lipid production. Our study provides basis for exploration of lichen-derived strains for biotechnological applications, and also benefits utilization of other nonconventional yeasts for sustainable production based on genome-based studies.
An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy
Authors: Kumar Anup , Cuccuru Gianmauro , Grüning Björn , Backofen Rolf
Published: April 2023

Background

Artificial intelligence (AI) programs that train on large datasets require powerful compute infrastructure consisting of several CPU cores and GPUs. JupyterLab provides an excellent framework for developing AI programs, but it needs to be hosted on such an infrastructure to enable faster training of AI programs using parallel computing.

Findings

An open-source, docker-based, and GPU-enabled JupyterLab infrastructure is developed that runs on the public compute infrastructure of Galaxy Europe consisting of thousands of CPU cores, many GPUs, and several petabytes of storage to rapidly prototype and develop end-to-end AI projects. Using a JupyterLab notebook, long-running AI model training programs can also be executed remotely to create trained models, represented in open neural network exchange (ONNX) format, and other output datasets in Galaxy. Other features include Git integration for version control, the option of creating and executing pipelines of notebooks, and multiple dashboards and packages for monitoring compute resources and visualization, respectively.

Conclusions

These features make JupyterLab in Galaxy Europe highly suitable for creating and managing AI projects. A recent scientific publication that predicts infected regions in COVID-19 computed tomography scan images is reproduced using various features of JupyterLab on Galaxy Europe. In addition, ColabFold, a faster implementation of AlphaFold2, is accessed in JupyterLab to predict the 3-dimensional structure of protein sequences. JupyterLab is accessible in 2 ways—one as an interactive Galaxy tool and the other by running the underlying Docker container. In both ways, long-running training can be executed on Galaxy’s compute infrastructure. Scripts to create the Docker container are available under MIT license at https://github.com/usegalaxy-eu/gpu-jupyterlab-docker.
Canine-inspired Unidirectional Flows for Improving Memory Effects in Machine Olfaction
Authors: Kim Soohwan , Mukherjee Sandeepan , Fonollosa Jordi , Hu David L
Published: April 2023

Synopsis

A dog's nose differs from a human's in that air does not change direction but flows in a unidirectional path from inlet to outlet. Previous simulations showed that unidirectional flow through a dog’s complex nasal passageways creates stagnant zones of trapped air. We hypothesize that these zones give the dog a “physical memory,” which it may use to compare recent odors to past ones. In this study, we conducted experiments with our previously built Gaseous Recognition Oscillatory Machine Integrating Technology (GROMIT) and performed corresponding simulations in two dimensions. We compared three settings: a control setting that mimics the bidirectional flow of the human nose; a short-circuit setting where odors exit before reaching the sensors; and a unidirectional configuration using a dedicated inlet and outlet that mimics the dog’s nose. After exposure to odors, the sensors in the unidirectional setting showed the slowest return to their baseline level, indicative of memory effects. Simulations showed that both short-circuit and unidirectional flows created trapped recirculation zones, which slowed the release of odors from the chamber. In the future, memory effects such as the ones found here may improve the sensitivity and utility of electronic noses.
Lax dynamics for Cartan decomposition with applications to Hamiltonian simulation
Authors: Chu Moody T
Published: April 2023

Simulating the time evolution of a Hamiltonian system on a classical computer is hard—The computational power required to even describe a quantum system scales exponentially with the number of its constituents, let alone integrate its equations of motion. Hamiltonian simulation on a quantum machine is a possible solution to this challenge—Assuming that a quantum system composing of spin-½ particles can be manipulated at will, then it is tenable to engineer the interaction between those particles according to the one that is to be simulated, and thus predict the value of physical quantities by simply performing the appropriate measurements on the system. Establishing a linkage between the unitary operators described mathematically as a logic solution and the unitary operators recognizable as quantum circuits for execution, is therefore essential for algorithm design and circuit implementation. Most current techniques are fallible because of truncation errors or the stagnation at local solutions. This work offers an innovative avenue by tackling the Cartan decomposition with the notion of Lax dynamics. Within the integration errors that is controllable, this approach gives rise to a genuine unitary synthesis that not only is numerically feasible, but also can be utilized to gauge the quality of results produced by other means, and extend the knowledge to a wide range of applications. This paper aims at establishing the theoretic and algorithmic foundations by exploiting the geometric properties of Hamiltonian subalgebras and describing a common mechanism for deriving the Lax dynamics.
Accumulation of Neutrophil Phagocytic Antibody Features Tracks With Naturally Acquired Immunity Against Malaria in Children
Authors: Nziza Nadege , Tran Tuan M , DeRiso Elizabeth A , Dolatshahi Sepideh , Herman Jonathan D , de Lacerda Luna , Junqueira Caroline , Lieberman Judy , Ongoiba Aissata , Doumbo Safiatou , Kayentao Kassoum , Traore Boubacar , Crompton Peter D , Alter Galit
Published: April 2023

Background

Studies have demonstrated the protective role of antibodies against malaria. Young children are known to be particularly vulnerable to malaria, pointing to the evolution of naturally acquired clinical immunity over time. However, whether changes in antibody functionality track with the acquisition of naturally acquired malaria immunity remains incompletely understood.

Methods

Using systems serology, we characterized sporozoite- and merozoite-specific antibody profiles of uninfected Malian children before the malaria season who differed in their ability to control parasitemia and fever following Plasmodium falciparum (Pf) infection. We then assessed the contributions of individual traits to overall clinical outcomes, focusing on the immunodominant sporozoite CSP and merozoite AMA1 and MSP1 antigens.

Results

Humoral immunity evolved with age, with an expansion of both magnitude and functional quality, particularly within blood-stage phagocytic antibody activity. Moreover, concerning clinical outcomes postinfection, protected children had higher antibody-dependent neutrophil activity along with higher levels of MSP1-specific IgG3 and IgA and CSP-specific IgG3 and IgG4 prior to the malaria season.

Conclusions

These data point to the natural evolution of functional humoral immunity to Pf with age and highlight particular antibody Fc-effector profiles associated with the control of malaria in children, providing clues for the design of next-generation vaccines or therapeutics.
Professional bodies
Authors: Friedman Andrew L , Afitska Natasha
Published: April 2023

Organization structures and processes of UK-based professional associations and regulatory bodies (professional bodies) are analyzed across all professions and over the long term. These are successful, long lived, and important organizations which have been neglected in the sociological and organizational literatures. Numbers have been growing and on average these organizations have enjoyed consistent financial success. They have been changing, reacting in part to external challenges, but also in response to internal challenges arising from growth and strains due to reactions to changes from their primary stakeholders, their members. We trace substantial changes in their staffing, governance, and education activities. We evaluate whether these changes amount to corporatization, as has been found in other public and third-sector organizations. We evaluate whether the changes confirm the charge that these organizations demonstrate the iron law of oligarchy. We find corporatization has been substantial but limited and that the changes represent shifting toward strategy rather than oligarchy, though democratic weakening has occurred. We find organization responses to member confusion, concerns, and criticisms to be influential in driving these changes and contributing to the sustainability of these organizations.
Preferred Reporting Items for Complex Sample Survey Analysis (PRICSSA)
Authors: Seidenberg Andrew B , Moser Richard P , West Brady T
Published: April 2023

Methodological issues pertaining to transparency and analytic error have been widely documented for publications featuring analysis of complex sample survey data. The availability of numerous public use datasets to researchers without adequate training in using these data likely contributes to these problems. In an effort to introduce standards for reporting analyses of survey data and promote replication, we propose the Preferred Reporting Items for Complex Sample Survey Analysis (PRICSSA), an itemized checklist to guide researchers publishing analyses using complex sample survey data. PRICSSA is modeled after other checklists (e.g., PRISMA, CONSORT) that have been widely adopted for other research designs. The PRICSSA items include a variety of survey characteristics, such as data collection dates, mode(s), response rate, and sample selection process. In addition, essential analytic information—such as sample sizes for all estimates, missing data rates and imputation methods (if applicable), disclosing if any data were deleted, specifying what survey weight and sample design variables were used along with method of variance estimation, and reporting design-adjusted standard errors/confidence intervals for all estimates—are also included. PRICSSA also recommends that authors make all corresponding software code available. Widespread adoption of PRICSSA will help improve the quality of secondary analyses of complex sample survey data through transparency and promote scientific rigor and reproducibility.
Safety and immunogenicity of ETVAX®, an oral inactivated vaccine against enterotoxigenic Escherichia coli diarrhoea: a double-blinded, randomized, placebo-controlled trial amongst Finnish travellers to Benin, West Africa
Authors: Kantele Anu , Riekkinen Marianna , Jokiranta T Sakari , Pakkanen Sari H , Pietilä Jukka-Pekka , Patjas Anu , Eriksson Mari , Khawaja Tamim , Klemets Peter , Marttinen Kati , Siikamäki Heli , Lundgren Anna , Holmgren Jan , Lissmats Agneta , Carlin Nils , Svennerholm Ann-Mari
Published: April 2023

Background

No licensed human vaccines are available against enterotoxigenic Escherichia coli (ETEC), a major diarrhoeal pathogen affecting children in low- and middle-income countries and foreign travellers alike. ETVAX®, a multivalent oral whole-cell vaccine containing four inactivated ETEC strains and the heat-labile enterotoxin B subunit (LTB), has proved promising in Phase 1 and Phase 1/ 2 studies.

Methods

We conducted a Phase 2b double-blinded, randomized, placebo-controlled trial amongst Finnish travellers to Benin, West Africa. This report presents study design and safety and immunogenicity data. Volunteers aged 18–65 years were randomized 1:1 to receive ETVAX® or placebo. They visited Benin for 12 days, provided stool and blood samples and completed adverse event (AE) forms. IgA and IgG antibodies to LTB and O78 lipopolysaccharide (LPS) were measured by electrochemiluminescence.

Results

The AEs did not differ significantly between vaccine (n = 374) and placebo (n = 375) recipients. Of the solicited AEs, loose stools/diarrhoea (26.7/25.9%) and stomach ache (23.0/20.0%) were reported most commonly. Of all possibly/probably vaccine-related AEs, the most frequent were gastrointestinal symptoms (54.0/48.8%) and nervous system disorders (20.3/25.1%). Serious AEs were recorded for 4.3/5.6%, all unlikely to be vaccine related. Amongst the ETVAX® recipients, LTB-specific IgA antibodies increased 22-fold. For the 370/372 vaccine/placebo recipients, the frequency of ≥2-fold increases against LTB was 81/2.4%, and against O78 LPS 69/2.7%. The majority of ETVAX® recipients (93%) responded to either LTB or O78.

Conclusions

This Phase 2b trial is the largest on ETVAX® undertaken amongst travellers to date. ETVAX® showed an excellent safety profile and proved strongly immunogenic, which encourages the further development of this vaccine.
Rare Hypermucoviscous Klebsiella pneumoniae Liver Abscess in an Active Duty Male Requiring Partial Liver Resection for Definitive Treatment
Authors: Michael Nicholas , Parascandola Salvatore , Saint-Laurent Stephanie , Brown Colin , Maddox John , Bradley Matthew , Learn Peter , Gage Michele
Published: April 2023

Antibiotics and drainage have largely replaced hepatic resection for the treatment of liver abscesses in the modern era; however, in cases caused by a rare strain of Klebsiella pneumoniae with a hypermucoviscous phenotype, more aggressive hepatic resection may be required. The patient is a 34-year-old male who presented to Landstuhl Regional Medical Center with a week of epigastric pain. His workup revealed a 6 cm liver abscess with growth to 10 cm in 48 hours. He underwent multiple drainage procedures at Landstuhl and then was transferred to Walter Reed where further surgical drainage was performed. Initial cultures demonstrated K. pneumoniae. He clinically improved and was able to discharge after a 2 week hospitalization. His final remaining surgical drain was removed as an outpatient, but 48 hours after removal, he was admitted to the intensive care unit in septic shock. Imaging revealed a 12 cm liver abscess, and cultures verified hypermucoviscous Klebsiella. After multidisciplinary discussion and counseling, he underwent an open right partial hepatectomy. Postoperatively he gradually recovered from his sepsis and major operation and then returned to his home in Landstuhl. This is a case of a rare hypermucoviscous variant of K. pneumoniae causing a liver abscess resistant to multiple drainage procedures, ultimately requiring open hepatic surgical resection for source control. This remains a last-resort option in the treatment of liver abscesses and should be considered early when caused by this rare strain of Klebsiella.
Infrared spectroscopy of the 2022 eruption of the recurrent nova U Sco
Authors: Evans A , Banerjee D P K , Woodward C E , Geballe T R , Gehrz R D , Page K L , Starrfield S
Published: April 2023

We present near-infrared spectroscopy of the 2022 eruption of the recurrent nova U Sco, over the period from 5.4 to 45.6 d after outburst. This is the most intensive infrared study of this nova. Our observations started early after the outburst and extended almost to the end of the ‘Super Soft’ X-ray phase. A major find is the presence of coronal lines from day 9.41, one of the earliest appearances of these in any nova, classical, or recurrent. The temperature of the coronal gas is 7 × 105 K. There is also evidence for the presence of much cooler ($\lesssim 2.5\times 10^4$  K) gas. Remarkable changes are seen in the He i 1.083 $\, \mu$ m line, the strength of which declines, then recovers, in anticorrelation with the X-ray behaviour. We conclude that shock ionization is the dominant excitation mechanism for the coronal line emission. There is evidence in the infrared spectra for the presence of black body emission at ∼20 000 K, which we tentatively identify with the irradiated secondary, and for free-free/free-bound emission. For the previously determined binary inclination of 82.7°, the implied ejection velocities are as high as 22 000 km s−1. These velocities appear unprecedented in nova outflows, and are comparable to those seen in supernovae, thereby marking U Sco as a truly remarkable object.
A robust and efficient algorithm for Chinese historical document analysis and recognition
Authors: Liu Chongyu , Jian Cheng , Huang Jiarong , Yang Wentao , Shi Yongxin , Jiang Qing , Jin Lianwen
Published: April 2023

This paper presents a novel and efficient algorithm for Chinese historical document understanding, incorporating three key components: a multi-oriented text detector, a dual-path learning-based text recognizer, and a heuristic-based reading order predictor.
Methane-to-chemicals: a pathway to decarbonization
Authors: Nesterenko Nikolai , Medeiros-Costa Izabel C , Clatworthy Edwin B , Cruchade Hugo , Konnov Stanislav V , Dath Jean-Pierre , Gilson Jean-Pierre , Mintova Svetlana
Published: April 2023

The utilization of methane for chemical production, often considered as the future of petrochemistry, historically could not compete economically with conventional processes due to higher investment costs. Achieving sustainability and decarbonization of the downstream industry by integration with a methane-to-chemicals process may provide an opportunity to unlock the future for these technologies. Gas-to-chemicals is an efficient tool to boost the decarbonization potential of renewable energy. While the current implementation of carbon capture utilization and storage (CCUS) technologies is of great importance for industrial decarbonization, a shift to greener CO2-free processes and CO2 utilization from external sources for manufacturing valuable goods is highly preferred. This review outlines potential options for how a methane-to-chemicals process could support decarbonization of the downstream industry.
Aggregation-induced emission biomaterials for anti-pathogen medical applications: detecting, imaging and killing
Authors: Zhang Zicong , Deng Ziwei , Zhu Lixun , Zeng Jialin , Cai Xu Min , Qiu Zijie , Zhao Zheng , Tang Ben Zhong
Published: April 2023

Microbial pathogens, including bacteria, fungi and viruses, greatly threaten the global public health. For pathogen infections, early diagnosis and precise treatment are essential to cut the mortality rate. The emergence of aggregation-induced emission (AIE) biomaterials provides an effective and promising tool for the theranostics of pathogen infections. In this review, the recent advances about AIE biomaterials for anti-pathogen theranostics are summarized. With the excellent sensitivity and photostability, AIE biomaterials have been widely applied for precise diagnosis of pathogens. Besides, different types of anti-pathogen methods based on AIE biomaterials will be presented in detail, including chemotherapy and phototherapy. Finally, the existing deficiencies and future development of AIE biomaterials for anti-pathogen applications will be discussed.
The Ti Plasmid, Driver of Agrobacterium Pathogenesis
Authors: Hooykaas Paul J. J.
Published: April 2023

The phytopathogenic bacterium Agrobacterium tumefaciens causes crown gall disease in plants, characterized by the formation of tumor-like galls where wounds were present. Nowadays, however, the bacterium and its Ti (tumor-inducing) plasmid is better known as an effective vector for the genetic manipulation of plants and fungi. In this review, I will briefly summarize some of the major discoveries that have led to this bacterium now playing such a prominent role worldwide in plant and fungal research at universities and research institutes and in agricultural biotechnology for the production of genetically modified crops. I will then delve a little deeper into some aspects of Agrobacterium biology and discuss the diversity among agrobacteria and the taxonomic position of these bacteria, the diversity in Ti plasmids, the molecular mechanism used by the bacteria to transform plants, and the discovery of protein translocation from the bacteria to host cells as an essential feature of Agrobacterium-mediated transformation.
The Academic Learning Health System: A Framework for Integrating the Multiple Missions of Academic Medical Centers
Authors: Rosenthal Gary E. , McClain Donald A. , High Kevin P. , Easterling Douglas , Sharkey Angela , Wagenknecht Lynne E. , O’Byrne Christopher , Woodside Rachel , Houston Thomas K.
Published: April 2023

The learning health system (LHS) has emerged over the past 15 years as a concept for improving health care delivery. Core aspects of the LHS concept include: promoting improved patient care through organizational learning, innovation, and continuous quality improvement; identifying, critically assessing, and translating knowledge and evidence into improved practices; building new knowledge and evidence around how to improve health care and health outcomes; analyzing clinical data to support learning, knowledge generation, and improved patient care; and engaging clinicians, patients, and other stakeholders in processes of learning, knowledge generation, and translation. However, the literature has paid less attention to how these LHS aspects may integrate with the multiple missions of academic medical centers (AMCs). The authors define an academic learning health system (aLHS) as an LHS built around a robust academic community and central academic mission, and they propose 6 features that emphasize how an aLHS differs from an LHS. An aLHS capitalizes on embedded academic expertise in health system sciences; engages the full spectrum of translational investigation from mechanistic basic sciences to population health; builds pipelines of experts in LHS sciences and clinicians with fluency in practicing in an LHS; applies core LHS principles to the development of curricula and clinical rotations for medical students, housestaff, and other learners; disseminates knowledge more broadly to advance the evidence for clinical practice and health systems science methods; and addresses social determinants of health, creating community partnerships to mitigate disparities and improve health equity. As AMCs evolve, the authors expect that additional differentiating features and ways to operationalize the aLHS will be identified and hope this article stimulates further discussion around the intersection of the LHS concept and AMCs.