bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reynolds Number Effects on Turbulent Wakes Generated by Rectangular Cylinders With Streamwise Aspect Ratios Between 1 and 4
Authors: Liu Manqi , Kumahor Sedem , Tachie Mark F. 
Published: September 2023

Abstract
The effects of streamwise aspect ratio and Reynolds number on the separated shear layer and near wake of rectangular cylinders in uniform flow are investigated experimentally using a particle image velocimetry system. Four length-to-height ratios (AR = 1, 2, 3, and 4) were examined at Reynolds numbers (based on freestream velocity and cylinder height) of 3000, 7200, 14,700, and 21,000. The results show that the separated shear layer is either shed directly into the wake region (AR1 and AR2) or reattaches onto the cylinder (AR4), regardless of the Reynolds number. Meanwhile, a transitional regime occurs for AR3 where mean flow reattachment on the cylinder is highly dependent on the Reynolds number. The peak magnitudes of the Reynolds stresses, turbulent kinetic energy, turbulence production, and its transport are highest for AR1 owing to stronger vortex shedding. Aspect ratio and Reynolds number also have significant effects on shear layer transitioning from laminar to turbulence but the transition lengths, when normalized by the corresponding value at Re = 3000, follow a universal power decay law. The wake characteristics, including the recirculation length and wake formation lengths, are independent of Reynolds number for AR1 but decrease with Reynolds number for the longer cylinders, while AR2 shows the largest values. The probability density functions and joint probability density functions are used to examine the effects of Reynolds number on the fluctuating velocities and momentum transport in the shear layer and near-wake region.
Effects of Hydraulic Parameters on the Retrieved Hydrothermal Dynamics of Unsaturated Soil Using a Synthetic Inverse Model
Authors: Lemoubou Ernest Léontin , Bogning Jean Roger 
Published: September 2023

Abstract
Hydraulic parameters are required indicators to quantify characteristic properties in agricultural fields. This technical brief analyses numerically the effects of soil hydraulic parameters on the retrieved responses of thermal, moisture, and solute dynamics using a synthetic inverse modeling. The goal was to provide analysis insight into the role of hydraulic parameters as tool for interpretation of soil thermal and hydrochemical responses. The inverse results show good agreement and present excellent accuracy when compared to the retrieved responses and true values. Several simulations reveal relevant contributions of the saturated hydraulic conductivity and moisture content, the shape parameter as well as the pore-size indicator on the special distributions of thermal and hydraulic responses.
On the Centennial of the Academic Careers (1919–2019) of Llewellyn M. K. Boelter and William H. McAdams: American Pioneers in Heat and Mass Transfer
Authors: Marner W. J. , Manglik Raj M. 
Published: September 2023

Abstract
In the early 1900s, the heat transfer state of the art in the United States of America (U.S.) lagged far behind that in Europe, especially in Germany. The initial 35 years of the 20th century, however, saw major changes take place as the process industry and other research institutions increasingly began requiring a better understanding of heat and mass transfer. While many individuals have since made important contributions to the field, both past and contemporary peers in the heat and mass transfer community have identified two pioneers as having played key roles in this effort in the U.S.: Llewellyn Michael Kraus Boelter of the University of California—Berkley (UC-Berkley) and the University of California—Los Angeles (UCLA), and William Henry McAdams of the Massachusetts Institute of Technology (MIT). They both started their respective academic positions in 1919, one on the East Coast and the other on the West Coast of U.S. In this paper, the centenary (1919–2019) of their seminal contributions is celebrated by highlighting the early heat and mass transfer developments in the U.S. and the careers of both McAdams and Boelter, which have been integral to this rich history. Many of their heat transfer contributions to the evolution of the field, up to the prevailing times in the 21st century, are documented, along with commentaries and annotations.
Novel bacterial topoisomerase inhibitors: unique targeting activities of amide enzyme-binding motifs for tricyclic analogs
Authors: Mann Chelsea A. , Carvajal Moreno Jessika J. , Lu Yanran , Dellos-Nolan Sheri , Wozniak Daniel J. , Yalowich Jack C. , Mitton-Fry Mark J. 
Published: September 2023

ABSTRACTAntimicrobial resistance has made a sizeable impact on public health and continues to threaten the effectiveness of antibacterial therapies. Novel bacterial topoisomerase inhibitors (NBTIs) are a promising class of antibacterial agents with a unique binding mode and distinct pharmacology that enables them to evade existing resistance mechanisms. The clinical development of NBTIs has been plagued by several issues, including cardiovascular safety. Herein, we report a sub-series of tricyclic NBTIs bearing an amide linkage that displays promising antibacterial activity, potent dual-target inhibition of DNA gyrase and topoisomerase IV (TopoIV), as well as improved cardiovascular safety and metabolic profiles. These amide NBTIs induced both single- and double-strand breaks in pBR322 DNA mediated byStaphylococcus aureusDNA gyrase, in contrast to prototypical NBTIs that cause only single-strand breaks. Unexpectedly, amides1aand1btargeted human topoisomerase IIα (TOP2α) causing both single- and double-strand breaks in pBR322 DNA, and induced DNA strand breaks in intact human leukemia K562 cells. In addition, anticancer drug-resistant K/VP.5 cells containing decreased levels of TOP2α were cross-resistant to amides1aand1b. Together, these results demonstrate broad spectrum antibacterial properties of selected tricyclic NBTIs, desirable safety profiles, an unusual ability to induce DNA double-stranded breaks, and activity against human TOP2α. Future work will be directed toward optimization and development of tricyclic NBTIs with potent and selective activity against bacteria. Finally, the current results may provide an additional avenue for development of selective anticancer agents.
Disrupting the infectious disease ecosystem in the digital precision health era innovations and converging emerging technologies
Authors: Abbo Lilian M. , Vasiliu-Feltes Ingrid 
Published: September 2023

ABSTRACT
This commentary explores the convergence of precision health and evolving technologies, including the critical role of artificial intelligence (AI) and emerging technologies in infectious diseases (ID) and microbiology. We discuss their disruptive impact on the ID ecosystem and examine the transformative potential of frontier technologies in precision health, public health, and global health when deployed with robust ethical and data governance guardrails in place.
Therapeutic potential of rWnt5A in curbing
Leishmania donovani
infection
Authors: Maity Shreyasi , Sengupta Soham , Sen Malini 
Published: September 2023

ABSTRACT

In view of the antagonism of Wnt5A signaling toward microbial pathogens, we were interested in evaluating the therapeutic potential of recombinant Wnt5A (rWnt5A) in curbing
Leishmania donovani
infection. Initially, using
L. donovani
-infected RAW 264.7 and peritoneal macrophages, we demonstrated that application of rWnt5A as opposed to the vehicle control to the infected cells significantly dampens
L. donovani
infection. Inhibition of infection was associated with increase in cell-associated reactive oxygen species (ROS), and blocked by the ROS production inhibitor diphenylene iodonium chloride (DPI). rWnt5A, but not the vehicle control (PBS: phosphate-buffered saline) administration to
L. donovani
-infected mice appreciably reduced the infection load, and inhibited disease progression as evident from the preservation of splenic white pulp architecture. rWnt5A administration, moreover, led to elevation of both cell-associated ROS and the activation of splenic T cells. Substantial increase in T cell-associated Interleukin-2 (IL-2) and Granzyme B (GRB) upon exposure of splenic lymphocytes harvested from rWnt5A-treated mice to
L. donovani
-infected RAW 264.7 macrophages
in vitro
validated the occurrence of
L. donovani
-responsive T cell activation
in vivo
. In summary, this study unveils the therapeutic potential of rWnt5A in curbing
L. donovani
infection and the progression of experimental visceral leishmaniasis possibly through increase in cellular ROS and T cell activation. Accordingly, it opens up a new avenue of investigation into the use of rWnt5A as a therapeutic agent for restraining the progression of drug-resistant
L. donovani
infection.
Roles of host SUMOylation in bacterial pathogenesis
Authors: Ma Xin , Zhao Chenhao , Xu Yuyao , Zhang Haifang 
Published: September 2023

ABSTRACT

Bacteria frequently interfere with the post-translational modifications of host cells to facilitate their survival and growth after invasion. SUMOylation, a reversible post-translational modification process, plays an important role in biological life activities. In addition to being critical to host cell metabolism and survival, SUMOylation also regulates gene expression and cell signal transmission. Moreover, SUMOylation in eukaryotic cells can be used by a variety of bacterial pathogens to advance bacterial invasion. In this minireview, we focused on the role and mechanism of host SUMOylation in the pathogenesis of six important clinical bacterial pathogens (
Listeria monocytogenes
,
Shigella flexneri
,
Salmonella
Typhimurium
, Klebsiella pneumoniae
,
Staphylococcus aureus
, and
Escherichia coli
). Taken together, this review provided new insights for understanding the unique pathogen-host interaction based on host SUMOylation and provided a novel perspective on the development of new strategies to combat bacterial infections in the future.
Early antibody treatment, inflammation, and risk of post-COVID conditions
Authors: Gebo Kelly A. , Heath Sonya L. , Fukuta Yuriko , Zhu Xianming , Baksh Sheriza , Abraham Allison G. , Habtehyimer Feben , Shade David , Ruff Jessica , Ram Malathi , Laeyendecker Oliver , Fernandez Reinaldo E. , Patel Eshan U. , Baker Owen R. , Shoham Shmuel , Cachay Edward R. , Currier Judith S. , Gerber Jonathan M. , Meisenberg Barry , Forthal Donald N. , Hammitt Laura L. , Huaman Moises A. , Levine Adam , Mosnaim Giselle S. , Patel Bela , Paxton James H. , Raval Jay S. , Sutcliffe Catherine G. , Anjan Shweta , Gniadek Thomas , Kassaye Seble , Blair Janis E. , Lane Karen , McBee Nichol A. , Gawad Amy L. , Das Piyali , Klein Sabra L. , Pekosz Andrew , Bloch Evan M. , Hanley Daniel , Casadevall Arturo , Tobian Aaron A. R. , Sullivan David J. ,   on behalf of the CSSC-004 Consortium
Published: September 2023

Post-COVID conditions (PCCs) are common and have significant morbidity. Risk factors for PCC include advancing age, female sex, obesity, and diabetes mellitus. Little is known about treatment, inflammation, and PCC. Among 882 individuals with confirmed SARS-CoV-2 infection participating in a randomized trial of COVID-19 convalescent plasma (CCP) vs control plasma with available biospecimens and symptom data, the association between early CCP treatment, cytokine levels, and PCC was evaluated. Cytokine and chemokine levels were assessed at baseline, day 14, and day 90 using a multiplexed sandwich immunoassay (Meso Scale Discovery). Presence of any self-reported PCC symptoms was assessed at day 90. Associations between CCP treatment, cytokine levels, and PCC were examined using multivariate logistic regression models. One third of the 882 participants had day 90 PCC symptoms, with fatigue (14.5%) and anosmia (14.5%) being most common. Cytokine levels decreased from baseline to day 90. In a multivariable analysis, female sex (adjusted odds ratio [AOR] = 2.69 [1.93–3.81]), older age (AOR = 1.32 [1.17–1.50]), and elevated baseline levels of IL-6 (AOR = 1.59 [1.02–2.47]) were independently associated with development of PCC. Those who received early CCP treatment (≤5 days after symptom onset) compared to late CCP treatment had statistically significant lower odds of PCC.

IMPORTANCE
Approximately 20% of individuals infected with SARS-CoV-2 experienced long-term health effects, as defined PCC. However, it is unknown if there are any early biomarkers associated with PCC or whether early intervention treatments may decrease the risk of PCC. In a secondary analysis of a randomized clinical trial, this study demonstrates that among outpatients with SARS-CoV-2, increased IL-6 at time of infection is associated with increased odds of PCC. In addition, among individuals treated early, within 5 days of symptom onset, with COVID-19 convalescent plasma, there was a trend for decreased odds of PCC after adjusting for other demographic and clinical characteristics. Future treatment studies should be considered to evaluate the effect of early treatment and anti-IL-6 therapies on PCC development.
Bacteriophages limitedly contribute to the antimicrobial resistome of microbial communities in wastewater treatment plants
Authors: Sabatino Raffaella , Sbaffi Tomasa , Sivalingam Periyasamy , Corno Gianluca , Fontaneto Diego , Di Cesare Andrea 
Published: September 2023

ABSTRACT

Bacteriophages are known as players in the transmission of antimicrobial resistance genes (ARGs) by horizontal gene transfer. In this study, we characterized the bacteriophage community and the associated ARGs to estimate the potential for phages to spread ARGs in aquatic ecosystems analyzing the intra- and extracellular DNA isolated from two wastewater treatment plants (WWTPs) by shotgun metagenomics. We compared the phage antimicrobial resistome with the bacterial resistome and investigated the effect of the final disinfection treatment on the phage community and its resistome. Phage community was mainly composed by
Siphoviridae
and other members of the order
Caudovirales
. The final disinfection only marginally affected the composition of the phage community, and it was not possible to measure its effect on the antimicrobial resistome. Indeed, only three phage metagenome-assembled genomes (pMAGs) annotated as
Siphoviridae
,
Padoviridae
, and
Myoviridae
were positive for putative ARGs. Among the detected ARGs, i.e.,
dfr
B6,
rpo
B mutants, and EF-Tu mutants, the first one was not annotated in the bacterial MAGs. Overall, these results demonstrate that bacteriophages limitedly contribute to the whole antimicrobial resistome. However, in order to obtain a comprehensive understanding of the antimicrobial resistome within a microbial community, the role of bacteriophages needs to be investigated.

IMPORTANCE
WWTPs are considered hotspots for the spread of ARGs by horizontal gene transfer. In this study, we evaluated the phage composition and the associated antimicrobial resistome by shotgun metagenomics of samples collected before and after the final disinfection treatment. Only a few bacteriophages carried ARGs. However, since one of the detected genes was not found in the bacterial metagenome-assembled genomes, it is necessary to investigate the phage community in order to gain a comprehensive overview of the antimicrobial resistome. This investigation could help assess the potential threats to human health.
Patient randomised controlled trial of technology enabled strategies to promote treatment adherence in liver transplantation: rationale and design of the TEST trial
Authors: Serper Marina , Burdzy Alexander , Schaubel Douglas E , Mason Richard , Banerjee Arpita , Goldberg David S , Martin Eric F , Mehta Shivan J , Russell Louise B , Cheung Amanda C , Ladner Daniela P , Yoshino Benavente Julia , Wolf Michael S 
Published: September 2023

Background and aimsLiver transplantation is a life-saving procedure for end-stage liver disease. However, post-transplant medication regimens are complex and non-adherence is common. Post-transplant medication non-adherence is associated with graft rejection, which can have long-term adverse consequences. Transplant centres are equipped with clinical staff that monitor patients post-transplant; however, digital health tools and proactive immunosuppression adherence monitoring has potential to improve outcomes.Methods and analysisThis is a patient-randomised prospective clinical trial at three transplant centres in the Northeast, Midwest and South to investigate the effects of a remotely administered adherence programme compared with usual care. The programme monitors potential non-adherence largely levering text message prompts and phenotypes the nature of the non-adhere as cognitive, psychological, medical, social or economic. Additional reminders for medications, clinical appointments and routine self-management support are incorporated to promote adherence to the entire medical regimen. The primary study outcome is medication adherence via 24-hour recall; secondary outcomes include additional medication adherence (ASK-12 self-reported scale, regimen knowledge scales, tacrolimus values), quality of life, functional health status and clinical outcomes (eg, days hospitalised). Study implementation, acceptability, feasibility, costs and potential cost-effectiveness will also be evaluated.Ethics and disseminationThe University of Pennsylvania Review Board has approved the study as the single IRB of record (protocol # 849575, V.1.4). Results will be published in peer-reviewed journals and summaries will be provided to study funders.Trial registration numberNCT05260268.
Refinement and validation of a comprehensive clinical diagnostic model (GAMAD) based on gender, age, multitarget circulating tumour DNA methylation signature and commonly used serological biomarkers for early detection of hepatocellular carcinoma: a multicentre, prospective observational study protocol
Authors: Yang Tian , Wang Nanya , Wang Fengmei , Liu Hongmei , Shen Feng , Lv Guoyue 
Published: September 2023

IntroductionPrompt detection of hepatocellular carcinoma (HCC) in patients with chronic liver diseases is critical for enhancing prognosis. Existing imaging techniques and serum markers fall short of clinical needs. This study aims to establish a non-invasive diagnostic model for early HCC detection in the Chinese population.Methods and analysisThis prospective, multicentre, observational study will enrol 2000 participants, including HCC patients, those with chronic liver diseases (hepatitis, cirrhosis and benign liver space-occupying lesions), and healthy individuals. The study will collect demographic data and blood samples, which will be used to test α-fetoprotein (AFP), des-γ-carboxy-prothrombin (DCP) and circulating tumour DNA (ctDNA) methylation. The GAMAD (Gender+Age+Methylation+AFP+DCP) model involving gender, age, ctDNA methylation signature, AFP and DCP will be developed and blindly validated in training and validation sets (1400 and 600 cases, respectively). Primary endpoints include sensitivity, specificity and accuracy (receiver operating characteristic curves; area under the curve value) of GAMAD for HCC and/or high-risk HCC groups. Secondary endpoints involve comparing GAMAD with the established GALAD (Gender+Age+AFP-L3+AFP+DCP) model and each blood index (AFP, DCP and methylation signature) to evaluate: (1) GAMAD’s clinical utility for HCC patients in all stages according to different staging systems; (2) GAMAD’s discrimination ability for patients in various subgroups, including liver cirrhosis (LC) related HCC and LC, hepatitis B virus (HBV) related HCC and HBV, hepatitis C virus (HCV) related HCC and HCV, and non-alcoholic fatty liver disease (NAFLD) related HCC and NAFLD.Ethics and disseminationThis trial has been approved by the Medical Ethics Committees of the First Hospital of Jilin University (#22K073-001), the Eastern Hepatobiliary Surgery Hospital, Naval Medical University (#EHBHKY2023-H0003-P001) and Tianjin Third Central Hospital (#IRB2023-007-01). All participants in the trial will provide written informed consent. Results of this study will be disseminated in peer-reviewed scientific journals and at conferences nationally and internationally.Trial registration numberNCT05626985.
Allotaxonometry and rank-turbulence divergence: a universal instrument for comparing complex systems
Authors: Dodds Peter Sheridan , Minot Joshua R. , Arnold Michael V. , Alshaabi Thayer , Adams Jane Lydia , Dewhurst David Rushing , Gray Tyler J. , Frank Morgan R. , Reagan Andrew J. , Danforth Christopher M. 
Published: September 2023

AbstractComplex systems often comprise many kinds of components which vary over many orders of magnitude in size: Populations of cities in countries, individual and corporate wealth in economies, species abundance in ecologies, word frequency in natural language, and node degree in complex networks. Here, we introduce ‘allotaxonometry’ along with ‘rank-turbulence divergence’ (RTD), a tunable instrument for comparing any two ranked lists of components. We analytically develop our rank-based divergence in a series of steps, and then establish a rank-based allotaxonograph which pairs a map-like histogram for rank-rank pairs with an ordered list of components according to divergence contribution. We explore the performance of rank-turbulence divergence, which we view as an instrument of ‘type calculus’, for a series of distinct settings including: Language use on Twitter and in books, species abundance, baby name popularity, market capitalization, performance in sports, mortality causes, and job titles. We provide a series of supplementary flipbooks which demonstrate the tunability and storytelling power of rank-based allotaxonometry.
Mapping between eras in scale-covariant gravity with a van der Waals cosmological source
Authors: Ribas M. O. , Bail L. C. , Devecchi F. P. 
Published: September 2023

In this paper, we apply the scale-covariant formalism established by Canuto et al. in order to connect different eras of fluid-driven universes. This technique depends on a scale function that can be adjusted by imposing different physical restrictions. In a previous work, Chaplygin fluid was considered as cosmological source; now a van der Waals constituent shows to be a consistent source to establish a mapping between an old decelerated-to-accelerated universe, ruled by Einstein equations, and an early universe, controlled by a modified gravitational theory. A similar situation emerges when a generalized Chaplygin fluid is considered. These cosmological properties are shown to be a direct consequence of an appropriate use of the scale-covariant technique, and can be seen as extensions of the original barotropic and plain Chaplygin cases.