bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gut commensalEnteroclosterspecies host inoviruses that are secretedin vitroandin vivo
Authors: Burckhardt Juan C. , Chong Derrick H.Y. , Pett Nicola , Tropini Carolina 
Published: October 2022

AbstractBackgroundBacteriophages in the familyInoviridae, or inoviruses, are under-characterized phages previously implicated in bacterial pathogenesis by contributing to biofilm formation, immune evasion, and toxin secretion. Unlike most bacteriophages, inoviruses do not lyse their host cells to release new progeny virions; rather, they encode a secretion system that actively pumps them out of the bacterial cell. To date, no inovirus associated with the human gut microbiome has been isolated or characterized.ResultsIn this study, we utilizedin silico, in vitroandin vivomethods to detect inoviruses in bacterial members of the gut microbiota. By screening a representative genome library of gut commensals, we detected inovirus prophages inEnterocloster spp. and we confirmed the secretion of inovirus particles inin vitrocultures of these organisms using imaging and qPCR. To assess how the gut abiotic environment, bacterial physiology, and inovirus secretion may be linked, we deployed a tripartitein vitroassay that progressively evaluated growth dynamics of the bacteria, biofilm formation, and inovirus secretion in the presence of changing osmotic environments. Counter to other inovirus-producing bacteria, inovirus production was not correlated with biofilm formation inEnterocloster spp. Instead, theEnteroclosterstrains’ inoviruses had heterogeneous responses to changing osmolality levels relevant to gut physiology. Notably, increasing osmolality induced inovirus secretion in a strain-dependent manner. We confirmed inovirus secretion in a gnotobiotic mouse model inoculated with individualEnteroclosterstrainsin vivoin unperturbed conditions. Furthermore, consistent with ourin vitroobservations, inovirus secretion was regulated by a changed osmotic environment in the gut due to osmotic laxatives.ConclusionIn this study, we report on the detection and characterization of novel inoviruses from gut commensals in theEnteroclostergenus. Together, our results demonstrate that human gut-associated bacteria can secrete inoviruses and begin to elucidate the environmental niche filled by inoviruses in commensal bacteria.
Development of serological assays to identifyHelicobacter suisandHelicobacter pyloriinfections
Authors: Matsui Hidenori , Rimbara Emiko , Suzuki Masato , Tokunaga Kengo , Suzuki Hidekazu , Sano Masaya , Ueda Takashi , Tsugawa Hitoshi , Nanjo Sohachi , Takeda Akira , Sasaki Makoto , Terao Shuichi , Suda Tsuyoshi , Aoki Sae , Shibayama Keigo , Ota Hiroyoshi , Mabe Katsuhiro 
Published: October 2022

SUMMARYHelicobacter suishosted by hogs is the most prevalent gastric non-Helicobacter pylori Helicobacterspecies found in humans. Recent studies suggest that theH. suisinfection has already induced many cases of gastric disease. However, the infection period and route ofH. suisfrom hogs remain unclear. Because diagnostic methods based on the urease activity ofH. suisoften yield negative judgments, there is no reliable method for diagnosingH. suisinfection in clinical practice without gastric biopsy specimens. We developed the world’s first ELISA to simultaneously diagnoseH. suisandH. pyloriinfection in a single test. The area under the ROC curve was 0.9648 or 0.9200 for identifyingH. suisorH. pyloriinfection, respectively. The sensitivity, specificity, and positive and negative predictive values for identifyingH. suisinfection were 100%, 92.6%, 76.9%, and 100%, and those for identifyingH. pyloriinfection were 88.2%, 87.5%, 65.2%, and 96.6%, respectively. (150 words)
Building Population Phenotypic Journeys from Laboratory Tests in Electronic Health Records for Translational Research
Authors: Zhang Xingmin A , Lee Kyeryoung , Jin Lan , Liu Zongzhi , Ai Lei , Jun Tomi , Higashi Mitch K. , Pan Qi , Oh William , Stolovitzky Gustavo , Schadt Eric , Robinson Peter N. , Wang Xiaoyan 
Published: October 2022

AbstractAbundant volumes of clinical laboratory test results available within Electronic health records (EHRs) are essential for differential diagnosis, treatment monitoring, and outcome evaluation. LOINC2HPO is a recently developed deep phenotyping approach to transform laboratory test results into the Human Phenotype Ontology (HPO) terms. Here, we deployed the approach on a large EHR dataset from the Sema4 Data Warehouse to build patient phenotypic journeys at scale. Among 1.07 billion laboratory test results, we successfully transformed 774 million (72.5%) into HPO-coded phenotypes and built a patient phenotypic journey for over 2.2 million patients. First, a global analysis of patient phenotypic journeys revealed a longitudinal increase in patients with genitourinary system abnormality. The analysis also revealed abnormal phenotypes with strong racial patterns. Second, using severe asthma as an example case, we identified abnormal phenotypes in the past three years that were correlated with asthma progression to severe state. Lastly, we demonstrated that converting laboratory test results into HPO terms resulted in limited information loss. Our study demonstrated that the phenotypic journey framework opens the way to characterize phenotypic trajectories in population level and screen biomarkers for translational research.
Rehabilitation in Survivors of COVID-19 (RE2SCUE): a non-randomized, controlled and open study
Authors: Campos Maria Cristine , Nery Tatyana , Speck Ana Elisa , Arpini Maiqueli , Antunes Moisés Moraes , de Bem Alves Ana Cristina , de Souza Santos Naiara , Matos Maria Paula Pereira , Junior Nelson Schmidt , Bicca Letícia Roehe , Panisson Camila Mascarelo , Freitas Mariana Alves , Diefenthaeler Fernando , Kuriki Heloyse Uliam , Damin Vanessa , Da Rosa Rodrigo Oliveira , Gress Josiane Bueno , Schneider Ione Jayce Ceola , Vieira Danielle Soares Rocha , Arcêncio Livia , Aguiar Aderbal Silva 
Published: October 2022

ABSTRACTThe sequelae of coronavirus disease-2019 (COVID-19) are another socio-economic problem of the pandemic. Fatigue and dyspnea are the most prevalent symptoms. It is not known whether exercise can be used to treat long COVID-19. This study aimed to investigate the effects of an 8-week face-to-face rehabilitation program on COVID-19 compared to a remote monitoring group. A total of 37 participants (24.3% hospitalized) were assessed before and after rehabilitation (n=22; 40.8±10.0 years) or remote monitoring (n=15; 45.4±10.5 years). The participants were allocated according to their preferences. Both groups showed improved fatigue and exercise capacity (Incremental Shuttle Walk Test). Participants in the face-to-face rehabilitation group showed improved dyspnea (Pulmonary Functional Status and Dyspnea Questionnaire), anxiety (Hospital Anxiety and Depression Scale), attention, and short-term memory (d2-R and Rey’s Auditory-Verbal Learning Test). Of the main sequelae, fatigue improves naturally, whereas dyspnea requires rehabilitation. Our results demonstrated the benefits of exercise for COVID-19 sequelae.
SPOP targets the immune transcription factor IRF1 for proteasomal degradation
Authors: Vunjak Milica , Schwartz Irene , Cantoran García Adriana , Mastrovito Marialaura , Hinterndorfer Matthias , de Almeida Melanie , Budroni Valentina , Wang Jingkui , Froussios Kimon , Jude Julian , Decker Thomas , Zuber Johannes , Versteeg Gijs A. 
Published: October 2022

AbstractAdaptation of the functional proteome is essential to counter pathogens during infection, yet precisely timed degradation of these response proteins after pathogen clearance is likewise key to preventing autoimmunity. Interferon Regulatory Factor 1 (IRF1) plays an essential role as a transcription factor in driving the expression of immune response genes during infection. The striking difference in functional output with other IRFs, is that IRF1 also drives the expression of various cell cycle inhibiting factors, making it an important tumor suppressor. Thus, it is critical to regulate the abundance of IRF1 to achieve a “Goldilocks” zone in which there is sufficient IRF1 to prevent tumorigenesis, yet not too much which could drive excessive immune activation. Using genetic screening, we identified the E3 ligase receptor Speckle Type BTB/POZ Protein (SPOP) to mediate IRF1 proteasomal turnover. We identified four S/T-rich degrons in IRF1 required for its SPOP MATH domain-dependent turnover. In the absence of SPOP, increased IRF1 protein levels functionally drive increased transcription of IRF1-response-genes, underpinning the biological significance of SPOP in curtailing IRF1 protein abundance.
WITHDRAWN: In-silico analysis of regulatory proteins involved in tricarboxylic acid cycle of Arabidopsis thaliana and structural analysis by Alphafold and other software
Authors: Nayab Hina , Asim Noreen , Shafique Farheen , ul Hassan Mahreen , Butt Sadia , Akbar Nazia 
Published: October 2022

Withdrawal StatementThe authors have withdrawn this manuscript because experiments are being repeated to validate the data. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Investigating the roles for essential genes in the regulation of the circadian clock inSynechococcus elongatususing CRISPR interference
Authors: Boodaghian Nouneh , Park Hyunsook , Cohen Susan E. 
Published: October 2022

ABSTRACTCircadian rhythms are approximately 24-hour cycles that allow organisms to anticipate predictable environmental changes such as light intensity, temperature, and humidity. Circadian rhythms are found widely throughout nature where cyanobacteria are the simplest organisms known to carry out circadian rhythmicity. Circadian rhythmicity in cyanobacteria is carried out via the KaiA, KaiB and KaiC core oscillator proteins that keep ~24h time. A series of input and output proteins; CikA, SasA and RpaA, regulate the clock by sensing environmental changes, and time rhythmic activities, including global rhythms of gene expression. Our previous work identified a novel set of KaiC-interacting proteins, some of which are encoded by genes that are essential for viability. To understand the relationship of these essential genes to the clock we applied CRISPR interference (CRISPRi) which utilizes a deactivated Cas9 protein and single guide RNA (sgRNA) to reduce the expression of target genes but not fully abolish their expression to allow for survival. Eight candidate genes were targeted, and strains were analyzed by quantitative Reverse Transcriptase (RT)-PCR for reduction of gene expression and rhythms of gene expression were monitored to analyze circadian phenotypes. We present data that reduced expression of SynPCC942_0001, which encodes for the β-clamp of the replicative DNA polymerase, or SynPCC7942_1081, which likely encodes for KtrA involved in K+transport, displayed a long circadian period compared to the wild type. As neither of these proteins have been previously implicated in the circadian clock, these data suggest that diverse cellular processes, DNA replication and K+transport, can influence the circadian clock and represent new avenues to understand clock function.
Genomic tracking of SARS-COV-2 variants in Myanmar
Authors: Oo Khine Zaw , Htun Zaw Win , Aung Nay Myo , Win Ko Ko , Htoo Sett Paing , Oo Thet Wai , Linn Kyaw Zawl , Aung Phyo Kyaw , Zaw Myo Thiha , Tun Kyaw Myo , Myint Kyee , Lwin Ko Ko 
Published: October 2022

AbstractBackgroundIn December 2019, the COVID-19 disease started in Wuhan, China. WHO declared a pandemic on March 12, 2020, and the disease started in Myanmar on March 23, 2020. December brought variants around the world, threatening the healthcare systems. To counter those threats, Myanmar started the COVID-19 variant surveillance program in late 2020.MethodsWhole genome sequencing was done six times between January 2021 and March 2022. We chose 83 samples with a PCR threshold cycle of less than 25. Then, we used MiSeq FGx for sequencing and Illumina DRAGEN COVIDSeq pipeline, command line interface, GISAID, and MEGA version 7 for data analysis.Result and DiscussionJanuary 2021 results showed no variant. The second run during the rise of cases in June 2021 showed multiple variants like Alpha, Delta, and Kappa. There is only Delta in the third run at the height of mortality in August, and Delta alone continued until the fourth run in December. After the world reported the Omicron variant in November, Myanmar started a surveillance program. The fifth run in January 2022 showed both Omicron and Delta variants. The sixth run in March 2022 showed only Omicron BA.2. Amino acid mutation at receptor binding domain (RBD) of Spike glycoprotein started since the second run coupling with high transmission, recurrence, and vaccine escape. We also found the mutation at the primer targets used in current RT-PCR platforms.ConclusionThe occurrence of multiple variants and mutations claimed vigilance at ports of entry and preparedness for effective control measures. Genomic surveillance with the observation of evolutionary data is required to predict imminent threats of the current disease and diagnose emerging infectious diseases.
A role for caveolar proteins in regulation of the circadian clock
Authors: Fonseka Sachini , Weger Benjamin D. , Weger Meltem , Martel Nick , Hall Thomas E. , Moradi Shayli Varasteh , Gabriel Christian H. , Kramer Achim , Ferguson Charles , Fernández-Rojo Manuel A. , Alexandrov Kirill , Rawashdeh Oliver , McMahon Kerrie-Ann , Gachon Frederic , Parton Robert G 
Published: October 2022

AbstractCaveolae are specialized invaginations of the plasma membrane that are formed by the co-assembly of caveolin integral membrane proteins and a cytoplasmic cavin coat complex. Previous work has proposed an interaction of the cavin coat protein, CAVIN3, with the key circadian clock protein, PER2. Here we show that cavin proteins can play a role in the regulation of the circadian clock by external stimuli. Loss ofCavin1in mice caused a shortening of the free-running period of locomotor activity. CAVIN1 and CAVIN3 were found to play a central role in core clock dynamics with either cavin protein directly interacting with PER2 and their perturbation leading to significant disruption in core clock mRNA expression and CRY1 protein oscillation. In cells, association of cavins and PER2 was increased upon caveola disassembly caused by oxidative stress or by calcium influx, stimuli linked to circadian clock regulation. We thus propose that the caveola system can play a modulatory role in circadian regulation through the cavin proteins.
The Enigma of UV Stress Granules: Research Challenges and New Perspectives
Authors: Cabral Alexandra J. , Costello Danielle C. , Farny Natalie G. 
Published: October 2022

AbstractStress granules (SGs) are non-membrane bound cytoplasmic condensates that form in response to a variety of different stressors. Canonical SGs are thought to have a cytoprotective role, reallocating cellular resources during stress by activation of the integrated stress response (ISR) to inhibit translation and avoid apoptosis. However, different stresses result in compositionally distinct, non-canonical SG formation that is likely pro-apoptotic, though the exact function(s) of both SGs subtypes remain unclear. A unique non-canonical SG subtype is triggered upon exposure to ultraviolet (UV) radiation. While it is generally agreed that UV SGs arebona fideSGs due to their dependence upon the core SG nucleating protein Ras GTPase-activating protein-binding protein 1 (G3BP1), the localization of other key components of UV SGs are unknown or under debate. Further, the dynamics of UV SGs are not known, though unique properties such as cell cycle dependence have been observed. This Perspective compiles the available information on SG subtypes and on UV SGs in particular in an attempt to understand the formation, dynamics, and function of these mysterious stress-specific complexes. We identify key gaps in knowledge related to UV SGs, and examine the unique aspects of their formation. We propose that more thorough knowledge of the distinct properties of UV SGs will lead to new avenues of understanding of the function of SGs, as well as their roles in disease.
Assessing the impact of a COVID-19 pandemic on supply chain transformation: an exploratory analysis
Authors: Min Hokey 
Published: October 2022

PurposeThis paper aims to examine how significantly the COVID-19 pandemic affects supply chain operations and how the firms have reacted to the COVID-19-induced supply chain crisis. In addition, this paper investigates whether the micro, small and medium enterprises (MSMEs) are affected disproportionally by the COVID-19-induced supply chain crisis.Design/methodology/approachThis paper developed a series of hypotheses and tested them using cross-tabulation, canonical correlation, discriminant and exploratory factor analyses of the empirical data.FindingsThe descriptive data analysis and hypothesis test results revealed that the labor productivity of the manufacturing, logistics and healthcare industry sectors was affected disproportionally by the COVID-19-induced crisis. However, outsourcing and global sourcing practices themselves did not necessarily exacerbate the severity of supply chain disruptions caused by COVID-19. The authors also found that MSMEs were adversely affected by the COVID-19 pandemic to a different degree than their large counterparts.Originality/valueThis paper is one of the first of its kind to assess the extent of the COVID-19 adverse impact on supply chain operations using the exploratory analysis of the data collected from the questionnaire survey of US firms representing various industries sectors.
Modeling tourists’ preference between hotels and peer-to-peer (P2P) sharing accommodation: a pre- and post-COVID-19 comparison
Authors: Ye Shun , Lei Sut Ieng , Zhao Xiaoyou , Zhu Lin , Law Rob 
Published: October 2022

Purpose
With the rapid development of sharing economy, travelers are facing choices between conventional hotels and the peer-to-peer sharing accommodation in urban tourism. The purpose of this study is to examine how travelers form their preferences in such choice situations and whether/how their preference formation mode would change with the COVID-19 pandemic.

Design/methodology/approach
A relative preference model was constructed and estimated for both domestic and outbound tourists, based on two waves of survey data collected before and after the COVID-19. The results of this study were compared to derive the evolution of preference formation patterns.

Findings
A set of 15 key value attributes and personal traits was identified, together with their differential effects with the pandemic. Their divergent effects between domestic and outbound trips were also delineated. Based on these findings, the competitive edges and advantageous market profiles were depicted for both hotel and sharing accommodation sectors.

Originality/value
This study contributes to the knowledge of tourists’ preference between accommodation types and adds empirical evidences to the impact of the pandemic on tourist behavior patterns. Both hotel and sharing accommodation practitioners can benefit from the findings to enhance their competitiveness.
ElGamal algorithm with hyperchaotic sequence to enhance security of cloud data
Authors: Koppaka Aruna Kumari , Lakshmi Vadlamani Naga 
Published: October 2022

Purpose
In the cloud-computing environment, privacy preservation and enabling security to the cloud data is a crucial and demanding task. In both the commercial and academic world, the privacy of important and sensitive data needs to be safeguarded from unauthorized users to improve its security. Therefore, several key generations, encryption and decryption algorithms are developed for data privacy preservation in the cloud environment. Still, the outsourced data remains with the problems like minimum data security, time consumption and increased computational complexity. The purpose of this research study is to develop an effective cryptosystem algorithm to secure the outsourced data with minimum computational complexity.

Design/methodology/approach
A new cryptosystem algorithm is proposed in this paper to address the above-mentioned concerns. The introduced cryptosystem algorithm has combined the ElGamal algorithm and hyperchaotic sequence, which effectively encrypts the outsourced data and diminishes the computational complexity of the system.

Findings
In the resulting section, the proposed improved ElGamal cryptosystem (IEC) algorithm performance is validated using the performance metrics like encryption time, execution time, decryption time and key generation comparison time. The IEC algorithm approximately reduced 0.08–1.786 ms of encryption and decryption time compared to the existing model: secure data deletion and verification.

Originality/value
The IEC algorithm significantly enhances the data security in cloud environments by increasing the power of key pairs. In this manuscript, the conventional ElGamal algorithm is integrated with the pseudorandom sequences for a pseudorandom key generation for improving the outsourced cloud data security.
The rhetoric of the Norwegian government and health authorities during the COVID-19 pandemic
Authors: Isaksson Maria , Solvoll Mona 
Published: October 2022

PurposeThe purpose of this study is to examine the identification and collaboration rhetoric of the Norwegian government and public health authorities during the pandemic. The aim is to show whether and how actors use strategies and themes of identification, and whether they build identification with their publics.Design/methodology/approachThe study combines qualitative and quantitative methods. Six identification strategies were identified through manual text analysis of press statements; word counts of each strategy were registered electronically to access quantitative data of individual actors.FindingsThe three strategies reflecting values, the two strategies reflecting division and disagreement and the strategy reflecting change showed almost equal frequencies. The strategy of shaping community, serving the function of change, and the division strategy, demonstrating identification through dissociation, were the most frequent strategies. Politicians preferred the collaboration strategy, while health experts preferred the strategy of concern and recognition.Originality/valueThe six identification strategies extend the understanding of leadership crisis communication and contemporary rhetoric as community-building discourse aiming for speaker–audience collaboration. The study demonstrates that division and disagreement are equally essential components of crisis communication as values and change. When actors differ in choice of strategy, themes and publics, they may still come across as coordinated and unified in their calls for solidarity, collective efforts and common understanding.