bluuebunny/crossref_metadata_2025_split huggingface dataset:
MXSGD alleviates CsA-induced hypoimmunity lung injury by regulating microflora metabolism
Authors: Ye Chun , Gao Zi han , Bie Zi-yi , Chen Kai-qin , Lu Fang guo , Wei Ke 
Published: January 2024

ContextMa Xing Shi Gan Decoction (MXSGD) is a traditional remedy for treating lung injuries that was developed by the Typhoid and Fever School of Pharmaceutical Biology. It has antitussive and expectorant effects, anti-inflammatory, antiviral, regulates the body’s immunity, etc.AimThe aim of this study is to investigate whether MXSGD can ameliorate cyclosporine A (CsA)-induced hypoimmunity lung injury by regulating microflora metabolism. Methods: Establishment of a model for CsA-induced hypoimmunity lung injury. Using 16S rRNA high-throughput sequencing and LC-MS, the effects of MXSGD on gut flora and lung tissue microecology of mice with CsA-induced hypoimmunity were investigated.ResultsMXSGD was able to preserve lung tissue morphology and structure, reduce serum inflammatory marker expression and protect against CsA-induced lung tissue damage. Compared to the model, MXSGD increased beneficial gut bacteria: Eubacterium ventriosum group and Eubacterium nodatum group; decreased intestinal pathogens: Rikenellaceae RC9 intestinal group; reduced the abundance of Chryseobacterium and Acinetobacter, promoted the production of Lactobacillus and Streptococcus, and then promoted the lung flora to produce short-chain fatty acids. MXSGD was able to enhance the expression of serum metabolites such as Americine, 2-hydroxyhexadecanoylcarnitine, Emetine, All-trans-decaprenyl diphosphate, Biliverdin-IX-alpha, Hordatin A and N-demethyl mifepristone in the CsA-induced hypoimmunity lung injury model.ConclusionMXSGD can restore gut and lung microbiota diversity and serum metabolite changes to inhibit inflammation, ameliorate CsA-induced hypoimmunity lung injury.
Calcification and trophic responses of mesophotic reefs to carbonate chemistry variability
Authors: Noyes Timothy J. , Garley Rebecca , Bates Nicholas R. 
Published: January 2024

Mesophotic coral ecosystems (MCEs) are extensions of adjacent shallow water coral reefs. Accessibility to these ecosystems is challenging due to their depth limits (~ 30 – 150 m) and as a result, scientific knowledge of these reef systems is limited. It has been posited that the depth limits of MCEs diminish anthropogenic effects experienced by shallow reef systems. A lack of empirical measurements to date has made this hypothesis impossible to determine for mesophotic reef metabolism. The alkalinity anomaly technique was utilized to determine rates of net ecosystem calcification (NEC) and net ecosystem production (NEP) from 30, 40 and 60 m mesophotic reefs during a 15-month period. Seawater chemistry was determined to be chemically conducive for calcification (average aragonite saturation Ωaragonite of 3.58, average calcite saturation Ωcalcite of 5.44) with estimates of NEC indicating these reef systems were net accretive and within global average values for shallow coral reefs (&lt; 30 m). The strongest periods of calcification occurred in late summer and were coupled with strong autotrophic signals. These episodes were followed by suppressed calcification and autotrophy and in the case of the 60 m reefs, a switch to heterotrophy. Whilst there was variability between the three reefs depths, the overall status of the mesophotic system was net autotrophic. This determination was the opposite of trophic status estimates previously described for adjacent shallow reefs. Whilst there were periods of net dissolution, the mesophotic reef system was net accretive (i.e., gross calcification &gt; gross CaCO3 dissolution). The measured inorganic carbon chemistry and estimates of NEC and NEP represent the first such biogeochemical measurements for MCEs. The values established by this study demonstrate just how close these understudied ecosystems are in terms of the known boundary thresholds for low saturation state reefs. Making predictions on how these ecosystems will respond to future climatic conditions, will require greater sampling effort over long times scales to decouple the environmental controls exerted on such ecosystems.
Family physicians overestimate diagnosis probabilities regardless of the test results
Authors: Ataç Ömer , Küçükali Hüseyin , Farımaz Ayşe Zülal Tokaç , Palteki Ayşe Seval , Çavdar Sabanur , Aslan Melek Nur , Atak Muhammed , Sezerol Mehmet Akif , Taşçı Yusuf , Hayran Osman 
Published: January 2024

IntroductionAs useful tools for clinical decision-making, diagnostic tests require careful interpretation in order to prevent underdiagnosis, overdiagnosis or misdiagnosis. The aim of this study was to explore primary care practitioners’ understanding and interpretation of the probability of disease before and after test results for six common clinical scenarios.MethodsThis cross-sectional study was conducted with 414 family physicians who were working at primary care in Istanbul via face-to-face interviews held between November 2021 and March 2022. The participants were asked to estimate the probability of diagnosis in six clinical scenarios provided to them. Clinical scenarios were about three cancer screening cases (breast, cervical and colorectal), and three infectious disease cases (pneumonia, urinary tract infection, and COVID-19). For each scenario participants estimated the probability of the diagnosis before application of a diagnostic test, after a positive test result, and after a negative test result. Their estimates were compared with the true answers derived from relevant guidelines.ResultsFor all scenarios, physicians’ estimates were significantly higher than the scientific evidence range. The minimum overestimation was positive test result for COVID-19 and maximum was pre-test case for cervical cancer. In the hypothetical control question for prevalence and test accuracy, physicians estimated disease probability as 95.0% for a positive test result and 5.0% for a negative test result while the correct answers were 2.0 and 0%, respectively (p &lt; 0.001).DiscussionComparing the scientific evidence, overestimation in all diagnostic scenarios, regardless of if the disease is an acute infection or a cancer, may indicate that the probabilistic approach is not conducted by the family physicians. To prevent inaccurate interpretation of the tests that may lead to incorrect or unnecessary treatments with adverse consequences, evidence-based decision-making capacity must be strengthened.
Emergency medicine pharmacotherapy compromises accuracy of plasma creatinine determination by enzyme-based methods: real-world clinical evidence and implications for clinical practice
Authors: Demlova Regina , Kozakova Sarka , Rihacek Michal , Buckova Dana , Horska Katerina , Wiewiorka Ondrej , Boucek Lubos , Selingerova Iveta , Podborska Martina , Korberova Alena , Mikuskova Alena , Starha Jiri , Benovska Miroslava , Radina Martin , Richter Michal , Zdrazilova Dubska Lenka , Valik Dalibor 
Published: January 2024

BackgroundAssessment of kidney function in emergency settings is essential across all medical subspecialties. Daily assessment of patient creatinine results from emergency medical services showed that some deviated from expected values, implying drug-related interference.MethodsReal-time clinical evaluation of an enzyme method (Roche CREP2) in comparison with the Jaffé gen. 2 method (Roche CREJ2) was performed. During the period of December 2022 and January 2023, we analyzed 8,498 patient samples, where 5,524 were heavily medicated STAT patient specimens, 500 were pediatric specimens, and 2,474 were from a distant general population in a different region using the same methods.ResultsIn 109 out of 5,524 hospital specimens (1.97%, p &lt; 0.001), the CREP2 value was apparently (25% or more) lower than CREJ2. Suspect interfering medication was found in a sample of 43 out of 46 reviewed patients where medication data were available. This phenomenon was not observed in the general population.ConclusionIn a polymedicated urgent care hospital population, a creatinine enzyme method produces unreliable results, apparently due to multiple drug-related interferences.
Novel and reported compensatory mutations in rpoABC genes found in drug resistant tuberculosis outbreaks
Authors: Conkle-Gutierrez Derek , Ramirez-Busby Sarah M. , Gorman Bria M. , Elghraoui Afif , Hoffner Sven , Elmaraachli Wael , Valafar Faramarz 
Published: January 2024

BackgroundRifampicin (RIF) is a key first-line drug used to treat tuberculosis, a primarily pulmonary disease caused by Mycobacterium tuberculosis. RIF resistance is caused by mutations in rpoB, at the cost of slower growth and reduced transcription efficiency. Antibiotic resistance to RIF is prevalent despite this fitness cost. Compensatory mutations in rpoABC genes have been shown to alleviate the fitness cost of rpoB:S450L, explaining how RIF resistant strains harbor this mutation can spread so rapidly. Unfortunately, the full set of RIF compensatory mutations is still unknown, particularly those compensating for rarer RIF resistance mutations.ObjectivesWe performed an association study on a globally representative set of 4,309 whole genome sequenced clinical M. tuberculosis isolates to identify novel putative compensatory mutations, determine the prevalence of known and previously reported putative compensatory mutations, and determine which RIF resistance markers associate with these compensatory mutations.Results and conclusionsOf the 1,079 RIF resistant isolates, 638 carried previously reported putative and high-probability compensatory mutations. Our strict criteria identified 46 additional mutations in rpoABC for which no strong prior evidence of their compensatory role exists. Of these, 35 have previously been reported. As such, our independent corroboration adds to the mounting evidence that these 35 also carry a compensatory role. The remaining 11 are novel putative compensatory markers, reported here for the first time. Six of these 11 novel putative compensatory mutations had two or more mutation events. Most compensatory mutations appear to be specifically compensating for the fitness loss due to rpoB:S450L. However, an outbreak of 22 closely related isolates each carried three rpoB mutations, the rare RIFR markers D435G and L452P and the putative compensatory mutation I1106T. This suggests compensation may require specific combinations of rpoABC mutations. Here, we report only mutations that met our very strict criteria. It is highly likely that many additional rpoABC mutations compensate for rare resistance-causing mutations and therefore did not carry the statistical power to be reported here. These findings aid in the identification of RIF resistant M. tuberculosis strains with restored fitness, which pose a greater risk of causing resistant outbreaks.
Simultaneous detection of human norovirus GI, GII and SARS-CoV-2 by a quantitative one-step triplex RT-qPCR
Authors: Yi Hua-Wei , Wang Xian-Mo , Tan Xin , Ding Cai-Zhi , Zhang Chang-Li , Wu Jia-Hao , Li Qi , Xin Chen-Qi , Fan Wen 
Published: January 2024

BackgroundThere are many similarities in the clinical manifestations of human norovirus and SARS-CoV-2 infections, and nucleic acid detection is the gold standard for diagnosing both diseases. In order to expedite the identification of norovirus and SARS-CoV-2, a quantitative one-step triplex reverse transcription PCR (RT-qPCR) method was designed in this paper.MethodsA one-step triplex RT-qPCR assay was developed for simultaneous detection and differentiation of human norovirus GI (NoV-GI), GII (NoV-GII) and SARS-CoV-2 from fecal specimens.ResultsThe triplex RT-qPCR assay had high detection reproducibility (CV &lt; 1%) and sensitivity. The lower limits of detection (LLOD95) of the triplex RT-qPCR assay for each target site were 128.5–172.8 copies/mL, and LLOD95 of the singleplex RT-qPCR assay were 110.3–142.0 copies/mL. Meanwhile, among the detection of clinical oropharyngeal swabs and fecal specimens, the results of the singleplex and triplex RT-qPCR assay showed high agreement.ConclusionThe triplex RT-qPCR assay for simultaneous detection of NoV-GI, NoV-GII and SARS-CoV-2 from fecal specimens has high clinical application value.
Impact of gut microbiota on nonalcoholic fatty liver disease: insights from a leave-one-out cross-validation study
Authors: Pan Tongtong , Su Lihuang , Zhang Yiying , Yi Fangfang , Chen Yongping 
Published: January 2024

IntroductionEnteric dysbacteriosis is strongly associated with nonalcoholic fatty liver disease (NAFLD). However, the underlying causal relationship remains unknown. Thus, the present study aimed to investigate the relationship between gut microbiota and NAFLD using Mendelian randomization (MR) and analyze the target genes potentially regulated by specific microbiota.MethodsBidirectional two-sample MR analysis was performed using inverse variance weighted (IVW) supplemented by MR-Egger, weighted median, simple mode, and weighted mode methods. Data were pooled from gut microbiota and NAFLD association studies. The least absolute shrinkage, selection operator regression, and the Support Vector Machine algorithm were used to identify genes regulated by these intestinal flora in NAFLD. The liver expression of these genes was verified in methionine choline-deficient (MCD) diet-fed mice.ResultsIVW results confirmed a causal relationship between eight specific gut microbes and NAFLD. Notably, the order Actinomycetales, NB1n, the family Actinomycetaceae, Oxalobacteraceae and the genus Ruminococcaceae UCG005 were positively correlated, whereas Lactobacillaceae, the Christensenellaceae R7 group, and Intestinibacter were negatively correlated with NAFLD onset. In NAFLD, these eight bacteria regulated four genes: colony-stimulating factor 2 receptor β, fucosyltransferase 2, 17-beta-hydroxysteroid dehydrogenase 14, and microtubule affinity regulatory kinase 3 (MAPK3). All genes, except MARK3, were differentially expressed in the liver tissues of MCD diet-fed mice.DiscussionThe abundance of eight gut microbiota species and NAFLD progression displayed a causal relationship based on the expression of the four target genes. Our findings contributed to the advancement of intestinal microecology-based diagnostic technologies and targeted therapies for NAFLD.
Neospora caninum surface antigen 1 is a major determinant of the pathogenesis of neosporosis in nonpregnant and pregnant mice
Authors: Abdelbaky Hanan H. , Rahman Md. Masudur , Shimoda Naomi , Chen Yu , Hasan Tanjila , Ushio Nanako , Nishikawa Yoshifumi 
Published: January 2024

IntroductionNcSAG1 is one of most widely investigated antigens of Neospora caninum in various research fields. Such studies demonstrated the proficiency of NcSAG1 in the regulatory process of parasite adhesion and invasion of host cells. Accordingly, the contribution of NcSAG1 to the pathogenesis of neosporosis can undoubtedly be extrapolated, but direct evidence is lacking. Herein, we provide the first successful attempt at the gene disruption of NcSAG1 and novel data on the invasion and virulence potentials of N. caninum in vitro and in vivo.MethodsThe disruption of the NcSAG1 gene was applied using the CRISPR/Cas9 system and confirmed by PCR, western blot and indirect fluorescent antibody tests as NcSAG1 knockout parasites (NcSAG1KO). Then, we investigated the role of NcSAG1 in the growth kinetics of the parasite in vitro.Results and discussionThe deletion of the NcSAG1 gene significantly decreased the infection rate and reduced the egress rate of the parasite. An in vivo study using nonpregnant female and male BALB/c mice revealed a significantly higher survival rate and lower body weight change in the group infected with the NcSAG1KO parasite than in the parental strain (Nc-1)-infected group. Regarding the vertical transmission model of BALB/c mice, the absence of the NcSAG1 gene significantly enhanced the survival of pups and greatly lowered the parasite burden in the brains of pups. In conclusion, our study suggested NcSAG1 as a key molecule in the pathogenesis of N. caninum.
Cognitive training for older prisoners: a qualitative analysis of prisoners’ and staff members’ perceptions
Authors: Verhülsdonk Sandra , Folkerts Ann-Kristin , Hasenberg Caroline , Bohn Claire , Christl Julia , Kalbe Elke , Krieger Theresia 
Published: January 2024

IntroductionCorrectional institutions are challenged by increasing numbers of older prisoners. Existing literature highlights the vulnerability of this group that is reflected by various somatic and mental health issues including cognitive dysfunctions. Although cognitive training studies in various target groups of older people have been conducted, there is lack of data regarding cognitive training in older prisoners. A structured cognitive group training program (“NEUROvitalis Prison”) with 12 weekly sessions was offered to male prisoners in Germany.MethodsPost intervention an exploratory qualitative study was conducted. Prisoners (N = 18) and staff (N = 4) perspectives were explored by conducting face-to-face semi-structured interviews. Audiotaped data were fully transcribed and deductive-inductive content analyses applied.ResultsBoth the prisoners and the staff perceived the cognitive training as very positive and stimulating. Moreover, the importance of the training was pronounced in terms of an increase in self-esteem and understanding of cognition and aging in the prisoners.DiscussionOur data indicate that cognitive training may be a feasible and valuable intervention for older prisoners that will be appreciated by both inmates and staff. The qualitative data provide substantial insight into the experiences with the applied cognitive training program. Moreover, valuable modifications for future conduct can be derived.
Development and deployment of a nationwide predictive model for chronic kidney disease progression in diabetic patients
Authors: Fu Zhiyan , Wang Zhiyu , Clemente Karen , Jaisinghani Mohit , Poon Ken Mei Ting , Yeo Anthony Wee Teo , Ang Gia Lee , Liew Adrian , Lim Chee Kong , Foo Marjorie Wai Yin , Chow Wai Leng , Ta Wee An 
Published: January 2024

AimChronic kidney disease (CKD) is a major complication of diabetes and a significant disease burden on the healthcare system. The aim of this work was to apply a predictive model to identify high-risk patients in the early stages of CKD as a means to provide early intervention to avert or delay kidney function deterioration.Materials and methodsUsing the data from the National Diabetes Database in Singapore, we applied a machine-learning algorithm to develop a predictive model for CKD progression in diabetic patients and to deploy the model nationwide.ResultsOur model was rigorously validated. It outperformed existing models and clinician predictions. The area under the receiver operating characteristic curve (AUC) of our model is 0.88, with the 95% confidence interval being 0.87 to 0.89. In recognition of its higher and consistent accuracy and clinical usefulness, our CKD model became the first clinical model deployed nationwide in Singapore and has been incorporated into a national program to engage patients in long-term care plans in battling chronic diseases. The risk score generated by the model stratifies patients into three risk levels, which are embedded into the Diabetes Patient Dashboard for clinicians and care managers who can then allocate healthcare resources accordingly.ConclusionThis project provided a successful example of how an artificial intelligence (AI)-based model can be adopted to support clinical decision-making nationwide.
A nomogram for the prediction of short-term mortality in patients with aneurysmal subarachnoid hemorrhage requiring mechanical ventilation: a post-hoc analysis
Authors: Mei Qing , Shen Hui , Liu Jian 
Published: January 2024

BackgroundAneurysmal subarachnoid hemorrhage (aSAH) is a devastating stroke subtype with high morbidity and mortality. Although several studies have developed a prediction model in aSAH to predict individual outcomes, few have addressed short-term mortality in patients requiring mechanical ventilation. The study aimed to construct a user-friendly nomogram to provide a simple, precise, and personalized prediction of 30-day mortality in patients with aSAH requiring mechanical ventilation.MethodsWe conducted a post-hoc analysis based on a retrospective study in a French university hospital intensive care unit (ICU). All patients with aSAH requiring mechanical ventilation from January 2010 to December 2015 were included. Demographic and clinical variables were collected to develop a nomogram for predicting 30-day mortality. The least absolute shrinkage and selection operator (LASSO) regression method was performed to identify predictors, and multivariate logistic regression was used to establish a nomogram. The discriminative ability, calibration, and clinical practicability of the nomogram to predict short-term mortality were tested using the area under the curve (AUC), calibration plot, and decision curve analysis (DCA).ResultsAdmission GCS, SAPS II, rebleeding, early brain injury (EBI), and external ventricular drain (EVD) were significantly associated with 30-day mortality in patients with aSAH requiring mechanical ventilation. Model A incorporated four clinical factors available in the early stages of the aSAH: GCS, SAPS II, rebleeding, and EBI. Then, the prediction model B with the five predictors was developed and presented in a nomogram. The predictive nomogram yielded an AUC of 0.795 [95% CI, 0.731–0.858], and in the internal validation with bootstrapping, the AUC was 0.780. The predictive model was well-calibrated, and decision curve analysis further confirmed the clinical usefulness of the nomogram.ConclusionWe have developed two models and constructed a nomogram that included five clinical characteristics to predict 30-day mortality in patients with aSAH requiring mechanical ventilation, which may aid clinical decision-making.
Changing handedness after nerve reconstruction in brachial plexus birth palsy
Authors: Yao Chenglun , Song Jie , Sun Jiayu , Tang Weijun , Chen Liang , Gu Yudong 
Published: January 2024

PurposeRight obstetric brachial plexus injuries (OBPI) often lead to left-handedness before limb function is restored post-surgery. A pertinent question arises about promoting a transition from left to right-handedness. We hypothesized that, with the decrease in neuroplasticity, handedness switching is not only difficult, but also reduces handedness-speech lateralization, impaired motor adaptability, and compromised language proficiency.MethodsWe retrospectively analyzed clinical data from January 1996 to January 2012 at our hospital. Participants were divided into intervention or control groups based on handedness switching. We compared handedness and computed lateral quotient (LQ) and lateralization index (LI) for handedness-speech center. Additionally, we assessed dominant hand’s writing speed, language function, and IQ. Associations between absolute LI and LQ values, writing speed, language scores, and IQ were examined.ResultsNineteen extended Erb’s palsy participants were enrolled, eight in the intervention group, and 11 in the control. No right-handed individuals were found in either cohort. The intervention group had significantly lower LQ and LI values, and fewer achieved normal writing speed. Yet, no notable disparities in language scores or IQ emerged. Notably, we established correlations between motor finesse, handedness degree, and handedness-speech lateralization.ConclusionFor right extended Erb’s palsy, shifting handedness is nearly unfeasible, and such an endeavor could trigger a reduction in handedness-speech lateralization magnitude and diminished motor finesse.