bluuebunny/crossref_metadata_2025_split huggingface dataset:
Laparoscopic cholecystectomy versus antibiotic therapy for acute cholecystitis in patients over 75 years: Randomized clinical trial and retrospective cohort study
Authors: Kivivuori Antti , Salminen Paulina , Ukkonen Mika , Ilves Imre , Vihervaara Hanna , Zalevskaja Kristina , Pajari Jenni , Paajanen Hannu , Rantanen Tuomo 
Published: August 2023

Background and objective: The prevalence of acute cholecystitis among elderly patients is increasing. The aim of this study was to compare laparoscopic cholecystectomy (LC) to antibiotics in elderly patients with acute cholecystitis. Methods: A randomized multicenter clinical trial including patients over 75 years with acute calculous cholecystitis was conducted in four hospitals in Finland between January 2017 and December 2019. Patients were randomized to undergo LC or antibiotic therapy. Due to patient enrollment challenges, the trial was prematurely terminated in December 2019. To assess all eligible patients, we performed a retrospective cohort study including all patients over 75 years with acute cholecystitis during the study period. The primary outcome was morbidity. Predefined secondary outcomes included mortality, readmission rate, and length of hospital stay. Results: Among 42 randomized patients (LC n = 24, antibiotics n = 18, mean age 82 years, 43% women), the complication rate was 17% (n = 4/24) after cholecystectomy and 33% (n = 6/18, 5/6 patients underwent cholecystectomy due to antibiotic treatment failure) after antibiotics (p = 0.209). In the retrospective cohort (n = 630, mean age 83 years, 49% women), 37% (236/630) of the patients were treated with cholecystectomy and 63% (394/630) with antibiotics. Readmissions were less common after surgical treatment compared with antibiotics in both randomized and retrospective cohort patients (8% vs 44%, p < 0.001% and 11 vs 32%, p < 0.001, respectively). There was no 30-day mortality within the randomized trial. In the retrospective patient cohort, overall mortality was 6% (35/630). Conclusions: LC may be superior to antibiotic therapy for acute cholecystitis in the selected group of elderly patients with acute cholecystitis.
The hidden cost of dalbavancin: OPAT RN time required in coordination for persons who use drugs
Authors: Douglass Alyse H. , Mayer Heather , Young Kathleen , Sikka Monica K. , Strnad Luke , Makadia Jina , Sukerman Ellie , Lewis James S. , Streifel Amber C. 
Published: August 2023

Background: Serious infections in persons who use drugs (PWUD) are rising. Dalbavancin, due to its extended half-life, offers an alternative treatment for patients in whom standard of care antibiotics are not feasible or practical, allowing for reduced hospital days and the avoidance of central line placement or the use of complex oral regimens. Objectives: We aim to describe the time and effort required for coordination of dalbavancin courses by outpatient registered nurses (RNs) and other outpatient parenteral antimicrobial therapy (OPAT) staff. Design and methods: We conducted a retrospective review of adult patients with documented substance use who received at least one dose of dalbavancin and quantified the number of interventions required by our OPAT RNs and other OPAT staff for coordination of dalbavancin courses. Additionally, detailed data on time spent per intervention were prospectively collected for a 1-month period. Results: A total of 52 patients with 53 dalbavancin courses were included. Most substance use was intravenous. Infectious diagnoses included bone and joint infections (61%) and endocarditis (7%), in addition to skin and soft tissue infections (19%). Infections were most commonly caused by Staphylococcus aureus (62%). RN intervention was required in the coordination of 60% of all courses and in 77% of courses in which at least one outpatient dose was needed. Adverse reactions occurred in one patient (2%) and 90-day readmissions due to infectious complications occurred in two patients (4%). Detailed time analysis was performed for seven consecutive patients, with a total of 179 min spent by OPAT RNs on coordination. Conclusions: The ease of dalbavancin administration does not eliminate the need for extensive RN coordination for successful administration of doses in the outpatient setting for PWUD. This need should be accounted for in program staffing to help increase successful dalbavancin course completion.
Effect of unintended short-term 3.0 g/day amoxicillin and probenecid treatment for early syphilis on patients with HIV-1 infection
Authors: Inada Makoto , Ando Naokatsu , Mizushima Daisuke , Kikuchi Yoshimi , Gatanaga Hiroyuki , Oka Shinichi 
Published: August 2023

Background: Standard therapy for early syphilis involves intramuscular injections of penicillin G, which frequently faces shortages in several countries. Fourteen-day amoxicillin therapy has been suggested as an alternative to benzathine penicillin G, but the optimal duration of amoxicillin therapy remains unclear and could theoretically be shortened to less than 14 days. The aim of this study was to explore the effectiveness of short-term amoxicillin therapy for early syphilis. Methods: We retrospectively explored the effectiveness of short-term amoxicillin therapy for early syphilis. The treatment data of patients who had received amoxicillin therapy for less than 14 days for unintended reasons were reviewed. Diagnosis was confirmed based on either the physician’s description or clinical presentation. Successful treatment was defined as a fourfold or greater decline in the rapid plasma reagin titer or sero-reversion to negative within 12 months. Results: Of 295 patients, 8 received short-term amoxicillin treatment. All were men who had sex with men and people living with human immunodeficiency virus. Their median age, CD4 count, and treatment duration were 34 years (range, 26–40), 258/mL (range, 112–930), and 9.5 days (range, 5–11), respectively. One patient had primary syphilis, six had secondary syphilis, and one had early latent syphilis. All patients, except one who showed reinfection, demonstrated a serological response within 4 months. The median time for serological response was 112 days. Conclusion: The results indicate that early syphilis could potentially be treated with 5–11 days of amoxicillin therapy combined with probenecid. This suggests that short-term amoxicillin therapy might be a sufficient treatment for early syphilis instead of the standard 14-day course.
Diagnostic utility of brain MRI in spontaneous intracerebral hemorrhage: A retrospective cohort study and meta-analysis
Authors: Wilson Mitch , Wang Jia-Yi , Andreev Alexander , Katsanos Aristeidis H , Selim Magdy , Lioutas Vasileios-Arsenios 
Published: August 2023

Introduction: The diagnostic yield of brain Magnetic Resonance Imaging (MRI) in spontaneous intracerebral hemorrhage (ICH) is unclear. We performed both an independent single-center retrospective cohort study and a meta-analysis to assess the detection rate of secondary lesions on MRI in patients with spontaneous ICH. Patients and methods: In the retrospective cohort study, we examined 856 consecutive patients with spontaneous ICH. Brain MRI scans on admission and follow-up were assessed for secondary lesions. We also examined clinical and CT radiographic variables associated with secondary lesions in univariable analysis. In the meta-analysis we searched PubMed and EMBASE for articles investigating the secondary lesion detection rate on brain MRI in spontaneous ICH. Results: Of the 856 patients with ICH, 481 (56%) had at least one brain BRI performed [70 ± 14 years, 270 (56% male)]. 462 (54%) had an admission MRI and 138 (16%) had both admission and follow-up MRIs. The detection rate of secondary lesions on admission MRIs was 24/462 (5.2%). 4/127 (3.1%) patients with a negative admission MRI had a lesion identified on follow-up MRI. No clinical or radiographic variables were associated with a secondary lesion on MRI using univariable analysis. The meta-analysis included five studies total (four identified in the PubMed and EMBASE searches and our cohort study) comprising 1147 patients with spontaneous ICH who underwent brain MRI. The pooled detection rate of secondary lesions was 11% (95% CI: 7–16). Discussion and conclusion: No predictors of secondary lesion detection were identified in our cohort study. Prospective studies are required to better understand the diagnostic utility of MRI in spontaneous ICH.
Republication of “Total Ankle Replacement Conversion to Tibiotalocalcaneal Arthrodesis With Bulk Femoral Head Allograft and Pseudoelastic Intramedullary Nail Providing Sustained Joint Compression”
Authors: Conklin Mark Jay , Smith Kathryn Elizabeth , Blair Jeremy Webster , Dupont Kenneth Michael 
Published: August 2023

Tibiotalocalcaneal (TTC) arthrodesis is commonly performed to salvage a failed total ankle replacement. These salvage procedures are complicated by significant bone loss from the ankle replacement and are associated with low patient satisfaction. Here, we describe 2 cases of patients who presented with a failed total ankle replacement and underwent arthrodesis using a bulk femoral head allograft and a novel pseudoelastic intramedullary nail. The intramedullary nail contains an internal pseudoelastic element that adapts to bone resorption and settling allowing for compression to be maintained at the arthrodesis sites throughout healing. In the first case, a 65-year-old woman with a failed total ankle replacement underwent TTC arthrodesis. The second case involved an obese 53-year-old woman who had previously undergone 2 total ankle replacement procedures that resulted in unsuccessful outcomes. In both cases, union was demonstrated on computed tomographic scan by 6 months. At 2 years postsurgery, both patients were satisfied with the procedure. These cases provide preliminary evidence that tibiotalocalcaneal arthrodesis with a pseudoelastic IM nail and structural allograft is an appropriate treatment for failed total ankle replacements. Level of Evidence: Level IV, therapeutic, case series.
An information-theoretic approach to single cell sequencing analysis
Authors: Casey Michael J. , Fliege Jörg , Sánchez-García Rubén J. , MacArthur Ben D. 
Published: August 2023

AbstractBackgroundSingle-cell sequencing (sc-Seq) experiments are producing increasingly large data sets. However, large data sets do not necessarily contain large amounts of information.ResultsHere, we formally quantify the information obtained from a sc-Seq experiment and show that it corresponds to an intuitive notion of gene expression heterogeneity. We demonstrate a natural relation between our notion of heterogeneity and that of cell type, decomposing heterogeneity into that component attributable to differential expression between cell types (inter-cluster heterogeneity) and that remaining (intra-cluster heterogeneity). We test our definition of heterogeneity as the objective function of a clustering algorithm, and show that it is a useful descriptor for gene expression patterns associated with different cell types.ConclusionsThus, our definition of gene heterogeneity leads to a biologically meaningful notion of cell type, as groups of cells that are statistically equivalent with respect to their patterns of gene expression. Our measure of heterogeneity, and its decomposition into inter- and intra-cluster, is non-parametric, intrinsic, unbiased, and requires no additional assumptions about expression patterns. Based on this theory, we develop an efficient method for the automatic unsupervised clustering of cells from sc-Seq data, and provide an R package implementation.
Structure and ecological function of the soil microbiome associated with ‘Sanghuang’ mushrooms suffering from fungal diseases
Authors: Xu Weifang , Sun Tao , Du Jiahui , Jin Shuqing , Zhang Ying , Bai Guofa , Li Wanyu , Yin Dengke 
Published: August 2023

Abstract
Background
The most serious challenges in medicinal ‘Sanghuang’ mushroom production are the fungal diseases caused by various molds. Application of biological agents has been regarded as a potential crop disease management strategy. Here, the soil microbiome associated with ‘Sanghuang’ mushroom affected by fungal diseases grown under field cultivation (FC) and hanging cultivation (HC) was characterized using culture-dependent and culture-independent methods.

Results
A total of 12,525 operational taxonomic units (OTUs) and 168 pure cultures were obtained using high-throughput sequencing and a culture-dependent method, respectively. From high-throughput sequencing, we found that HC samples had more OTUs, higher α-diversity, and greater microbial community complexity than FC samples. Analysis of β-diversity divided the soil microbes into two groups according to cultivation mode. Basidiomycota (48.6%) and Ascomycota (46.5%) were the two dominant fungal phyla in FC samples, with the representative genera Trichoderma (56.3%), Coprinellus (29.4%) and Discosia (4.8%), while only the phylum Ascomycota (84.5%) was predominant in HC samples, with the representative genera Discosia (34.0%), Trichoderma (30.2%), Penicillium (14.9%), and Aspergillus (7.8%). Notably, Trichoderma was predominant in both the culture-independent and culture-dependent analyses, with Trichoderma sp. FZ0005 showing high host pathogenicity. Among the 87 culturable bacteria, 15 exhibited varying extents of antifungal activity against Trichoderma sp. FZ0005, with three strains of Bacillus spp. (HX0037, HX0016, and HX0039) showing outstanding antifungal capacity.

Conclusions
Overall, our results suggest that Trichoderma is the major causal agent of ‘Sanghuang’ fungal diseases and that Bacillus strains may be used as biocontrol agents in ‘Sanghuang’ cultivation.
Plant GARDEN: a portal website for cross-searching between different types of genomic and genetic resources in a wide variety of plant species
Authors: Ichihara Hisako , Yamada Manabu , Kohara Mitsuyo , Hirakawa Hideki , Ghelfi Andrea , Tamura Takuro , Nakaya Akihiro , Nakamura Yasukazu , Shirasawa Sachiko , Yamashita Samatchaya , Toda Yosuke , Harada Daijiro , Fujishiro Tsunakazu , Komaki Akiko , Fawcett Jeffrey A. , Sugihara Eiji , Tabata Satoshi , Isobe Sachiko N. 
Published: August 2023

Abstract
Background
Plant genome information is fundamental to plant research and development. Along with the increase in the number of published plant genomes, there is a need for an efficient system to retrieve various kinds of genome-related information from many plant species across plant kingdoms. Various plant databases have been developed, but no public database covers both genomic and genetic resources over a wide range of plant species.

Main body
We have developed a plant genome portal site, Plant GARDEN (Genome And Resource Database Entry: https://plantgarden.jp/en/index), to provide diverse information related to plant genomics and genetics in divergent plant species. Elasticsearch is used as a search engine, and cross-keyword search across species is available. Web-based user interfaces (WUI) for PCs and tablet computers were independently developed to make data searches more convenient. Several types of data are stored in Plant GARDEN: reference genomes, gene sequences, PCR-based DNA markers, trait-linked DNA markers identified in genetic studies, SNPs, and in/dels on publicly available sequence read archives (SRAs). The data registered in Plant GARDEN as of March 2023 included 304 assembled genome sequences, 11,331,614 gene sequences, 419,132 DNA markers, 8,225 QTLs, and 5,934 SNP lists (gvcf files). In addition, we have re-annotated all the genes registered in Plant GARDEN by using a functional annotation tool, Hayai-Annotation, to compare the orthologous relationships among genes.

Conclusion
The aim of Plant GARDEN is to provide plant genome information for use in the fields of plant science as well as for plant-based industries, education, and other relevant areas. Therefore, we have designed a WUI that allows a diverse range of users to access such information in an easy-to-understand manner. Plant GARDEN will eventually include a wide range of plant species for which genome sequences are assembled, and thus the number of plant species in the database will continue to expand. We anticipate that Plant GARDEN will promote the understanding of genomes and gene diversity by facilitating comparisons of the registered sequences.
PRedicting the EVolution of SubjectIvE Cognitive Decline to Alzheimer’s Disease With machine learning: the PREVIEW study protocol
Authors: Mazzeo Salvatore , Lassi Michael , Padiglioni Sonia , Vergani Alberto Arturo , Moschini Valentina , Scarpino Maenia , Giacomucci Giulia , Burali Rachele , Morinelli Carmen , Fabbiani Carlo , Galdo Giulia , Amato Lorenzo Gaetano , Bagnoli Silvia , Emiliani Filippo , Ingannato Assunta , Nacmias Benedetta , Sorbi Sandro , Grippo Antonello , Mazzoni Alberto , Bessi Valentina 
Published: August 2023

Abstract
Background
As disease-modifying therapies (DMTs) for Alzheimer's disease (AD) are becoming a reality, there is an urgent need to select cost-effective tools that can accurately identify patients in the earliest stages of the disease. Subjective Cognitive Decline (SCD) is a condition in which individuals complain of cognitive decline with normal performances on neuropsychological evaluation. Many studies demonstrated a higher prevalence of Alzheimer’s pathology in patients diagnosed with SCD as compared to the general population. Consequently, SCD was suggested as an early symptomatic phase of AD. We will describe the study protocol of a prospective cohort study (PREVIEW) that aim to identify features derived from easily accessible, cost-effective and non-invasive assessment to accurately detect SCD patients who will progress to AD dementia.

Methods
We will include patients who self-referred to our memory clinic and are diagnosed with SCD. Participants will undergo: clinical, neurologic and neuropsychological examination, estimation of cognitive reserve and depression, evaluation of personality traits, APOE and BDNF genotyping, electroencephalography and event-related potential recording, lumbar puncture for measurement of Aβ42, t-tau, and p-tau concentration and Aβ42/Aβ40 ratio. Recruited patients will have follow-up neuropsychological examinations every two years. Collected data will be used to train a machine learning algorithm to define the risk of being carriers of AD and progress to dementia in patients with SCD.

Discussion
This is the first study to investigate the application of machine learning to predict AD in patients with SCD. Since all the features we will consider can be derived from non-invasive and easily accessible assessments, our expected results may provide evidence for defining cost-effective and globally scalable tools to estimate the risk of AD and address the needs of patients with memory complaints. In the era of DMTs, this will have crucial implications for the early identification of patients suitable for treatment in the initial stages of AD.

Trial registration number (TRN)
NCT05569083.
Impact and burden of sickle cell disease in critically ill obstetric patients in a high dependency unit in Sierra Leone—a registry based evaluation
Authors: Mortara Milena , Turay Momoh Sitta , Boyle Sonia , Caracciolo Claudia , Bah Sarjoh , Kargbo Henry , Hanciles Eva , John-Cole Valerie , Scapini Ester , Benoni Roberto , Dissanayake Vishmi , Beane Abi , Haniffa Rashan , Adetunji Adeniji O. , Taylor Williamson , Pisani Luigi 
Published: August 2023

Abstract
Introduction
Sickle cell disease (SCD) in pregnancy is associated with worse maternal and neonatal outcomes. There is limited available data describing the burden and outcomes of critically ill obstetric patients affected by SCD in low-income settings.

Objectives
We aimed to define SCD burden and impact on mortality in critically-ill obstetric patients admitted to an urban referral hospital in Sierra Leone. We hypothesized that SCD burden is high and independently associated with increased mortality.

Methods
We performed a registry-based cross-sectional study from March 2020 to December 2021 in the high-dependency unit (HDU) of Princess Christian Maternity Hospital PCMH, Freetown. Primary endpoints were the proportion of patients identified in the SCD group and HDU mortality. Secondary endpoints included frequency of maternal direct obstetric complications (MDOCs) and the maternal early obstetric warning score (MEOWS).

Results
Out of a total of 497 patients, 25 (5.5%) qualified to be included in the SCD group. MEOWS on admission was not different between patients with and without SCD and SCD patients had also less frequently reported MDOCs. Yet, crude HDU mortality in the SCD group was 36%, compared to 9.5% in the non SCD group (P < 0.01), with an independent association between SCD group exposure and mortality when accounting for severity on admission (hazard ratio 3.40; 95%CI 1.57—7.39; P = 0.002). Patients with SCD had a tendency to longer HDU length of stay.

Conclusions
One out of twenty patients accessing a HDU in Sierra Leone fulfilled criteria for SCD. Despite comparable severity on admission, mortality in SCD patients was four times higher than patients without SCD. Optimization of intermediate and intensive care for this group of patients should be prioritized in low-resource settings with high maternal mortality.
Analysis of factors associated with the umbilical cord pitch value by ultrasound measurement in late pregnancy
Authors: Liang Chen , Xu Youfeng 
Published: August 2023

Abstract
Background
This study aimed to investigate the factors associated with the antenatal umbilical cord pitch value by ultrasound measurement in late pregnancy. We investigated the factors associated with the umbilical cord pitch value under prenatal ultrasound measurement.

Methods
This study included 528 pregnant women who underwent routine antenatal ultrasound examinations in Ningbo Women and Children’s Hospital from December 2020 to August 2021. Their umbilical cord pitch values and diameter, Wharton’s jelly thickness, amniotic fluid indexes, umbilical artery blood flow parameters, and other relevant data, such as ages and gestational ages, were measured. Information about delivery methods, placenta, umbilical cord, and neonatal weight were recorded during follow-up. Statistical analysis was performed on the above data, and the factors associated with the pitch values were analyzed by linear regression.

Results
This study revealed that cord torsion (p < 0.001, 95% confidence interval [CI]=-34.81 to -19.01), cord entanglement (p < 0.001, 95% CI = 10.71 to 20.11), thickening of Wharton’s jelly (p = 0.001, 95% CI = 5.39 to 20.24), and cord edema (p = 0.015, 95%CI = 2.09 to 19.44), gestational age (p = 0.024, 95%CI = 0.14 to 1.89), age of pregnant woman (p = 0.009, 95%CI= -1.15 to -0.16), and neonatal weight (p = 0.011, 95%CI = 0.002 to 0.012) were significantly correlated with the pitch values.

Conclusion
The umbilical cord pitch value significantly correlated with cord entanglement, cord torsion, cord edema, Wharton’s jelly thickening, gestational age, age of the pregnant woman, and neonatal weight. Notably, the pitch value by prenatal ultrasound measurement is predictive of cord morphological abnormalities such as cord entanglement, cord torsion, cord edema, and Wharton’s jelly thickening.