bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation, characterization, and genetic manipulation of cold-tolerant, manganese-oxidizing
Pseudomonas
sp. strains
Authors: Jones Ian , Vermillion Duncan , Tracy Chase , Denton Robert , Davis Rick , Geszvain Kati 
Published: August 2024

ABSTRACT

Manganese-oxidizing bacteria (MnOB) produce Mn oxide minerals that can be used by humans for bioremediation, but the purpose for the bacterium is less clear. This study describes the isolation and characterization of cold-tolerant MnOB strains isolated from a compost pile in Morris, Minnesota, USA:
Pseudomonas
sp. MS-1 and DSV-1. The strains were preliminarily identified as members of species
Pseudomonas psychrophila
by 16S rRNA analysis and a multi-locus phylogenetic study using a database of 88 genomes from the
Pseudomonas
genus. However, the average nucleotide identity between these strains and the
P. psychrophila
sp. CF149 type strain was less than 93%. Thus, the two strains are members of a novel species that diverged from
P. psychrophila
. DSV-1 and MS-1 are cold tolerant; both grow at 4°C but faster at 24°C. Unlike the mesophilic MnOB
P. putida
GB-1, both strains are capable of robustly oxidizing Mn at low temperatures. Both DSV-1 and MS-1 genomes contain homologs of several Mn oxidation genes found in
P. putida
GB-1 (
mnxG
,
mcoA
,
mnxS1
,
mnxS2,
and
mnxR
). Random mutagenesis by transposon insertion was successfully performed in both strains and identified genes involved in Mn oxidation that were similar to those found in
P. putida
GB-1. Our results show that MnOB can be isolated from compost, supporting a role for Mn oxidation in plant waste degradation. The novel isolates
Pseudomonas
spp. DSV-1 and MS-1 both can oxidize Mn at low temperature and likely employ similar mechanisms and regulation as
P. putida
GB-1.

IMPORTANCE

Biogenic Mn oxides have high sorptive capacity and are strong oxidants. These two characteristics make these oxides and the microbes that make them attractive tools for the bioremediation of wastewater and contaminated environments. Identifying MnOB that can be used for bioremediation is an active area of research. As cold-tolerant MnOB,
Pseudomonas
sp. DSV-1 and MS-1 have the potential to expand the environmental conditions in which biogenic Mn oxide bioremediation can be performed. The similarity of these organisms to the well-characterized MnOB
P. putida
GB-1 and the ability to manipulate their genomes raise the possibility of modifying them to improve their bioremediation ability.
Association between different levels of suppressed viral load and the risk of sexual transmission of HIV among serodiscordant couples on antiretroviral therapy: a protocol for a two-step systematic review and individual participant data meta-analysis
Authors: Djiadeu Pascal , Begum Housne , Archibald Chris , Ekmekjian Taline , Busa Giovanna , Dansoh Jeffery , Van Nguyen Phu , Fleurant Annie 
Published: August 2024

IntroductionHIV is a major global public health issue. The risk of sexual transmission of HIV in serodiscordant couples when the partner living with HIV maintains a suppressed viral load of <200 copies of HIV copies/mL has been found in systematic reviews to be negligible. A recent systematic review reported a similar risk of transmission for viral load<1000 copies/mL, but quantitative transmission risk estimates were not provided. Precise estimates of the risk of sexual transmission at sustained viral load levels between 200 copies/mL and 1000 copies/mL remain a significant gap in the literature.Methods and analysisA systematic search of various electronic databases for the articles written in English or French will be conducted from January 2000 to October 2023, including MEDLINE, Embase, the Cochrane Central Register of Controlled Trials via Ovid and Scopus. The first step of a two-step meta-analysis will consist of a systematic review along with a meta-analysis, and the second step will use individual participant data for meta-analysis. Our primary outcome is the risk of sexual HIV transmission in serodiscordant couples where the partner living with HIV is on antiretroviral therapy. Our secondary outcome is the dose-response association between different levels of viral load and the risk of sexual HIV transmission. We will ascertain the risk of bias using the Risk Of Bias in Non-randomised Studies of Interventions (ROBINS-I) and Quality in Prognostic Studies (QUIPS), the risk of publication bias using forest plots and Egger’s test and heterogeneity using I2. A random effects model will estimate the pooled incidence of sexual HIV transmission, and multivariate logistic regression will be used to assess the viral load dose-response relationships. The Grading of Recommendations, Assessment, Development and Evaluation system will determine the certainty of evidence.Ethics and disseminationThe meta-analysis will be conducted using deidentified data. No human subjects will be involved in the research. Findings will be disseminated through peer-reviewed publications, presentations and conferences.PROSPERO registration numberCRD42023476946.
Pandemic lessons on essential healthcare services for the urban poor: a qualitative perspective of users and providers in Bangladesh
Authors: Hasan A M Rumayan , Hasan Md Zahid , Ahmed Mohammad Wahid , Selim Mohammad Abdus , Rabbani Md Golam , Rasheed Sabrina , Reidpath Daniel D , Mahmood Shehrin Shaila 
Published: August 2024

ObjectiveThe COVID-19 pandemic imposed unprecedented challenges to health systems globally. This study explored slum dwellers’ experience of receiving essential health services during the pandemic and the challenges faced by healthcare providers in urban areas of Bangladesh.DesignThe study followed a cross-sectional study design using qualitative methods.SettingThe study was conducted in Dhaka and Gazipur City Corporations during November 2020–February 2021.Participants17 key informant interviews were carried out with healthcare providers and policy-makers and 22 in-depth interviews were carried out with slum dwellers. Thematic analysis was performed.ResultsThe study identified challenges to the provision of essential healthcare in selected areas of Dhaka and Gazipur City Corporations during the COVID-19 pandemic. The lack of information on the availability of functional healthcare facilities, fear of contracting COVID-19 and restrictions on movement and transportation, resulted in delays in seeking essential healthcare during a pandemic. Access to healthcare facilities was further hindered by various hospitals’ decision to refuse care to general patients without valid, negative COVID-19 test results. Healthcare providers identified patients’ tendency to hide COVID-19 symptoms as a barrier to providing healthcare services to general patients. Conversely, patients concealed their symptoms to avoid COVID-19 tests and gain access to required treatment. In addition, the reallocation of human resources for COVID-19 treatment disrupted the delivery of essential health services.ConclusionThe pandemic affected the accessibility of the slum population to essential healthcare and disrupted health service delivery. The findings of the study have highlighted gaps in the health system during an emergency response period like COVID-19. The study will assist the government and other stakeholders in designing tailored interventions and allocating resources in a more efficient manner to ensure universal health coverage in the face of health emergencies.
Probing the black holes in a dark matter halo of M87 using gravitational wave echoes
Authors: Liu Dong , Yang Yi , Long Zheng-Wen 
Published: August 2024

AbstractVariations at the event horizon structure of a black hole will emit the signals of the gravitational wave echoes associated with the ringdown of the binary black hole merger. In this work, combining mass model of M87 and Einasto profile for dark matter halo, we construct one formal solution of black holes in dark matter halo, and this solution includes the regular black hole for geometric parameter $$a < 2M$$

a
<
2
M

and the wormhole for $$a \ge 2M$$

a
≥
2
M

. Then, we test this solution under axial gravitational perturbation and calculate their quasinormal modes (QNM). Our results show that when geometric parameter $$a>2M$$

a
>
2
M

, a series of gravitational wave echoes appear after the QNM, and one distinctive feature of gravitational wave echoes is the double barrier. Besides, we also study the impacts of shape parameters $$\alpha $$
α
of Einasto profile both on the QNM and gravitational wave echoes, and extract their frequencies using WKB method and Prony method. In principle, with the increasing of shape parameter $$\alpha $$
α
, the frequencies of the QNM and gravitational wave echoes between the different shape parameters must be different. But now there is zero difference of the frequencies between shape parameter $$\alpha =0.18$$

α
=
0.18

and $$\alpha =0.20$$

α
=
0.20

. Zero difference is not allowed, so we give an upper limit for shape parameter $$\alpha $$
α
, which is approximately $$\alpha <0.18$$

α
<
0.18

. These signals of gravitational wave echoes in a dark matter halo may be detected in the near future, and these characteristics of gravitational wave echoes may serve as local measurements of dark matter.
Hybrid quantum key distribution: A novel approach for secure end-to-end communication in network infrastructure
Authors: Ali Sellami 
Published: August 2024

The Quantum Key Distribution (QKD) network approach has emerged as a promising solution and has garnered significant interest across various domains. QKD networks can be broadly categorized into two main types: those based on measurement-device-dependent (MDD) protocols and those based on measurement-device-independent (MDI) protocols. A novel network scheme is proposed combining these two protocols to guarantee end-to-end secure communication. It comprises two interconnected networks — the first uses a measurement-device-dependent protocol to connect routers with nearby nodes, while the second employs a measurement-device-independent protocol to interconnect the routers. In the first network, the process begins with Alice (Router) generating two types of weak quantum signals — the first has intensity, frequency and polarization or phase randomly varied, while the second with different delay times. Alice randomly transmits either signal states carrying information or decoy states with varying properties to the receivers (Bobs) over the quantum channels. She also sends a synchronization signal along with the quantum signals. At the receiver end, the synchronization pulse timestamps the incoming quantum signals. Each Bob then randomly shifts the frequencies of the received signals and measures their phase/polarization of the first signal and measures the delay times of the second signal. The secret key is derived by combining the frequency, the delay time and the phase/polarization information of the quantum signals, resulting in longer key lengths. Encoding information across multiple degrees of freedom enables extended key generation for secure communication. However, between the routers, MDI-QKD protocols are used to securely share the keys. This hybrid approach aims to ensure secure end-to-end communication across the network.
Investigating the genetic relationship of intracranial and subcortical brain volumes with depression and other psychiatric disorders
Authors: García-Marín Luis M. , Ogonowski Natalia S. , Han Laura K.M. , Maya-Martínez Mateo , Mitchell Brittany L. , Schmaal Lianne , Martin Nicholas G. , Rentería Miguel E. 
Published: August 2024

Abstract
Depression is one of the most common mental health disorders worldwide, yet its neurobiological mechanisms remain poorly understood. Structural brain differences in subcortical limbic regions are thought to be implicated in the pathology of depression. We leveraged genome-wide association studies (GWAS) summary-level data to explore the molecular pathways underlying the relationship between genetic risk for depression and intracranial and subcortical brain volumes measured via magnetic resonance imaging. At the whole-genome level, we identified a negative genetic correlation (rG) between depression and the volume of the ventral diencephalon (rG = -0.08), which remained significant after adjusting for multiple testing. We observed nominal (P &lt; 0.05) positive genetic correlations between depression and the volumes of the caudate nucleus (rG = 0.06) and the putamen (rG = 0.06), while hippocampal volume displayed a negative genetic correlation (rG = -0.06) with depression. Pairwise GWAS analyses uncovered 104 genome segments with genetic variants influencing the aetiology of depression and at least one brain volume at the local genetic level. Gene association analyses of these genomic segments suggest putative links with dopamine neurotransmission, mesocorticolimbic functional connectivity, GABAergic transmission, and the insulin signalling pathway. Sensitivity analyses showed that the volume of the ventral diencephalon is also negatively correlated with bipolar disorder and schizophrenia; however, most of the genes associated with depression and brain volumes are specific for depression and do not replicate when investigating bipolar disorder or schizophrenia with brain volumes. We observed negative phenotypic correlations between depression and intracranial and subcortical brain volumes. Overall, our findings contribute to our understanding of the neurobiology of depression and suggest that, besides the known role of the hippocampus, other subcortical structures might also play essential roles in the aetiology of depression.
Should We Pass the Great Filter?
Authors: Harmsen Maaike Eline , van den Brink Gijsbert 
Published: August 2024

Abstract
This paper provides a Christian philosophical and theological response to the moral imperative of human advancement through multiplanetarism as emerging from the Great Filter theory. First, it explains the Fermi paradox that underlies the Great Filter theory. Next, it explores this theory itself and its motivational power in driving advancement toward multiplanetarism. In particular, we explore two motives behind the multiplanetary efforts that are (in part) guided by the Great Filter theory, analyzing the relevant statements of SpaceX founder and chief engineer Elon Musk. Finally, we assess these motivations (and the accompanying normative assumptions) behind space exploration and multiplanetarism from the perspective of Reformational philosophy, using Herman Dooyeweerd’s theory of ground motives as a lens. Thus, the paper’s leading research question is this: How can we assess the current attempts at securing a multiplanetary existence for humankind in the light of Dooyeweerd’s theory of ground motives?
Ukraine’s Parliament during Wartime
Authors: Ivasyk Stanislav 
Published: August 2024

Abstract
The article examines the challenge of balancing security restrictions with the need for transparent and democratic legislative functioning. It begins by highlighting the importance of transparency and its relationship with democracy and good governance. Using Ukraine as a case study, the article reviews the open data and other transparency measures employed by Ukraine’s Parliament before the onset of the full-scale Russian aggression on February 24, 2022. It then discusses the limitations imposed on these measures following the declaration of martial law, the ensuing public debate, and subsequent modifications to specific transparency restrictions. Through concrete examples, the paper argues that a lack of transparency and the failure to balance security limitations with public demand for openness can undermine the parliament’s legitimacy and constitutional authority. The article concludes that security measures must be proportionate and regularly updated to preserve the integrity of parliamentary democracy and the constitutional role of the parliament.
Painful Ankle due to Impingement Between the Medial Malleolus and Navicular
Authors: Nischal Neha , Iyengar Karthikeyan P. , Botchu Rajesh 
Published: August 2024

Introduction: A plethora of pathologies can cause medial ankle pain. Material and methods: We present a case of 66-year-old male with medial ankle pain. Result: Bilateral CTEV (Congenital talipes equino varus) with impingement between the navicular and medial malleolus was present, which was contributing to medial ankle pain. Conclusion: One needs to be aware of this rare form of impingement in patients with medial ankle pain.
Heartware ventricular assist device versus HeartMate II versus HeartMate III in advanced heart failure patients: A systematic review and meta-analysis
Authors: Hanafy Dudy Arman , Husen Theresia Feline , Angelica Ruth , Nathania Ilona , Trianita Suwatri Widya , Lintangella Pasati , Erdianto Wahyu Prima , Prasetyo Prisillia 
Published: August 2024

Objective:Ventricular assist device is one of the treatment options for heart failure patients. Therefore, the purpose of this review is to aid in clinical decision-making of exchanging previous older ventricular assist device models to the newest one, HM3.Methods:The search was conducted across several databases until February 25, 2023, and was registered with the ID of CRD42023405367. Risk of bias was performed using Cochrane Risk of Bias 2.0 and the Newcastle Ottawa Scale. In order to rank and evaluate the pooled odds ratios and mean differences with 95% confidence intervals, we employed conventional and Bayesian network meta-analysis converted to surface under the cumulative ranking.Results:A total of 49 studies with 31,105 patients were included in this review. HM3 is the best device exchange choice that causes the lowest risk of mortality (HM3 (99.98) > HM2 (32.43) > HVAD (17.58)), cerebrovascular accidents (HM3 (99.99) > HM2 (42.41) > HVAD (7.60)), other neurologic events beside cerebrovascular accident (HM3 (91.45) > HM2 (54.16) > HVAD (4.39)), pump thrombosis (HM3 (100.00) > HM2 (39.20) > HVAD (10.80)), and bleeding (HM3 (97.12) > HM2 (47.60) > HVAD (5.28)). HM3 is also better than HM2 in hospital admissions (OR: 1.90 (95% CI: 1.15–3.12)). When complications were present, HM2 or Heartware ventricular assist devices exchange to HM3 lowered the mortality rate compared to exchanging it to the same device type.Conclusion:HM3 is the best device for all six outcomes. Exchange from Heartware ventricular assist devices or HM2 to HM3 rather than the same ventricular assist device type is recommended only if a complication is present.
TubIAgnosis: A machine learning-based web application for active tuberculosis diagnosis using complete blood count data
Authors: Ghermi Mohamed , Messedi Meriam , Adida Chahira , Belarbi Kada , Djazouli Mohamed El Amine , Berrazeg Zahia Ibtissem , Kallel Sellami Maryam , Ghezini Younes , Louati Mahdi 
Published: August 2024

Objective Tuberculosis remains a major global health challenge, with delayed diagnosis contributing to increased transmission and disease burden. While microbiological tests are the gold standard for confirming active tuberculosis, many cases lack microbiological evidence, necessitating additional clinical and laboratory data for diagnosis. The complete blood count (CBC), an inexpensive and widely available test, could provide a valuable tool for tuberculosis diagnosis by analyzing disturbances in blood parameters. This study aimed to develop and evaluate a machine learning (ML)-based web application, TubIAgnosis, for diagnosing active tuberculosis using CBC data. Methods We conducted a retrospective case-control study using data from 449 tuberculosis patients and 1200 healthy controls in Oran, Algeria, from January 2016 to April 2023. Eight ML algorithms were trained on 18 CBC parameters and demographic data. Model performance was evaluated using balanced accuracy, sensitivity, specificity, positive predictive value, negative predictive value, and area under the receiver operating characteristic curve (AUC). Results The best-performing model, Extreme Gradient Boosting (XGB), achieved a balanced accuracy of 83.3%, AUC of 89.4%, sensitivity of 83.3%, and specificity of 83.3% on the testing dataset. Platelet-to-lymphocyte ratio was the most influential parameter in this ML predictive model. The best performing model (XGB) was made available online as a web application called TubIAgnosis, which is available free of charge at https://yh5f0z-ghermi-mohamed.shinyapps.io/TubIAgnosis/ . Conclusions TubIAgnosis, a ML-based web application utilizing CBC data, demonstrated promising performance for diagnosing active tuberculosis. This accessible and cost-effective tool could complement existing diagnostic methods, particularly in resource-limited settings. Prospective studies are warranted to further validate and refine this approach.
Family Medicine Physician Readiness to Treat Behavioral Health Conditions: A Mixed Methods Study
Authors: Chea Ashlyn , Heo Moonseong , Zeller Timothy Aaron 
Published: August 2024

Introduction: Behavioral and mental health conditions present significant challenges in the United States where access to care is limited. Family medicine physicians play a crucial role in addressing these challenges, often serving as frontline clinicians for behavioral and mental health conditions. Methods: This study examined the current behavioral and mental health system in a predominantly rural 10-county region in the Southeastern United States through gap analysis in addition to a survey of preparedness and barriers among family medicine physicians in the region. Results: Gap analysis results indicated that (1) stigma and lack of accessible education about behavioral and mental health, (2) fragmented resources, (3) inaccessible care, and (4) workforce shortage and burnout were primary drivers of poor outcomes in the region. Survey results indicated that physicians feel prepared to treat anxiety and depression but feel less prepared to manage bipolar disorder, schizophrenia, and substance use disorders. Respondents disagreed that there are adequate local resources and referral options for patients with behavioral and mental health conditions. Lack of timely access, distance, cost/insurance status, were all cited by respondents as barriers to appropriate care. Conclusion and Recommendations: Findings underscore the importance of supporting family medicine physicians to enhance behavioral and mental healthcare outcomes. Behavioral health integration in primary care settings is a promising strategy to improve care accessibility and clinician preparedness. Bridging gaps in health care outcomes requires collaborative efforts, enhanced training, and policy advocacy within the family medicine community to ensure comprehensive and equitable behavioral and mental healthcare delivery.