bluuebunny/crossref_metadata_2025_split huggingface dataset:
MpTGA, together with MpNPR, regulates sexual reproduction and independently affects oil body formation in Marchantia polymorpha
Authors: Gutsche Nora , Koczula Jens , Trupp Melanie , Holtmannspötter Michael , Appelfeller Melanie , Rupp Oliver , Busch Andrea , Zachgo Sabine 
Published: December 2023

Summary
In angiosperms, basic leucine‐zipper (bZIP) TGACG‐motif‐binding (TGA) transcription factors (TFs) regulate developmental and stress‐related processes, the latter often involving NON EXPRESSOR OF PATHOGENESIS‐RELATED GENES (NPR) coregulator interactions. To gain insight into their functions in an early diverging land‐plant lineage, the single MpTGA and sole MpNPR genes were investigated in the liverwort Marchantia polymorpha.
We generated Marchantia MpTGA and MpNPR knockout and overexpression mutants and conducted morphological, transcriptomic and expression studies. Furthermore, we investigated MpTGA interactions with wild‐type and mutagenized MpNPR and expanded our analyses including TGA TFs from two streptophyte algae.
Mptga mutants fail to induce the switch from vegetative to reproductive development and lack gametangiophore formation. MpTGA and MpNPR proteins interact and Mpnpr mutant analysis reveals a novel coregulatory NPR role in sexual reproduction. Additionally, MpTGA acts independently of MpNPR as a repressor of oil body (OB) formation and can thereby affect herbivory.
The single MpTGA TF exerts a dual role in sexual reproduction and OB formation in Marchantia. Common activities of MpTGA/MpNPR in sexual development suggest that coregulatory interactions were established after emergence of land‐plant‐specific NPR genes and contributed to the diversification of TGA TF functions during land‐plant evolution.
Essential amino acid requirements of fish and crustaceans, a meta‐analysis
Authors: Xing Shujuan , Liang Xiaofang , Zhang Xiaoran , Oliva‐Teles Aires , Peres Helena , Li Min , Wang Hao , Mai Kangsen , Kaushik Sadasivam J. , Xue Min 
Published: December 2023

AbstractA meta‐analysis of literature data on essential amino acid (EAA) requirements of fish and crustaceans was performed to re‐estimate EAA requirements and provide ideal amino acid profiles. Large numbers of studies have been conducted on EAA requirements of fish and crustaceans over the past decades. However, estimated EAA requirements of different species showed a large variation due to differences in methodological approaches and regression models. An extensive search and inclusion of literature on EAA requirements were conducted following the Preferred Reporting Items for Systematic Reviews and Meta‐Analyses guidelines in this study, resulting in a dataset of 358 studies covering 77 species. The relative percentage of maximum weight gain was used as the outcome to evaluate the 10 EAA requirements. Forest plots analysis was employed for heterogeneity analysis, study weight allocation and re‐estimation of the requirements. Results showed that trophic level, water temperature and dietary EAA inclusion levels affected EAA requirements estimation. The meta‐analysis suggested that the estimated 10 EAA requirements (expressed as % crude protein, CP) of the fish were: arginine (Arg) 5.0 (±0.14), histidine (His) 2.0 (±0.11), isoleucine (Ile) 3.3 (±0.16), leucine (Leu) 4.9 (±0.24), valine (Val) 3.8 (±0.11), lysine (Lys) 5.2 (±0.12), sulfur amino acids (Met + Cys) 3.5 (±0.18), total aromatic amino acids (Phe + Tyr) 6.2 (±0.12), threonine (Thr) 3.5 (±0.18) and tryptophan (Trp) 0.9 (±0.08). Estimated EAA requirements (expressed as % CP) of crustaceans were Arg 5.1 (±0.31), His 2.5 (±0.15), Ile 4.3 (±0.97), Leu 5.7 (±0.08), Val 4.3 (±0.30), Lys 4.9 (±0.28), Met + Cys 3.2 (±0.18), Phe + Tyr 5.1 (±0.65), Thr 3.8 (±0.04) and Trp 0.8 (±0.15).
Ultrasound‐guided thread lifting for the prevention of parotid gland and diagnosing parotid duct complications
Authors: Kim Ji Soo , Yang Eun‐Jung , Kim Woo‐Ram , Lee Won , Kim Hee‐Jin , Yi Kyu‐Ho 
Published: December 2023

AbstractBackgroundThread lifting is a common minimally invasive plastic surgery procedure. Parotid gland injury caused by thread lifting is a known complication; however, visual evidence of this complication is lacking.ObjectivesThis study aimed to present cases of parotid gland injury by thread lifting shown using ultrasound and to discuss the importance of ultrasound detection of the location of the parotid gland before thread insertion.MethodsThis study included eight patients diagnosed with parotid gland perforation and one with parotid duct injury due to threads from November 2020 to October 2022.ResultsSix patients showed tenderness and swelling, three were asymptomatic, and one with duct injury showed severe swelling and pain. Although the severity and duration of symptoms have differed, we confirmed the progress of improvement with conservative treatment and confirmed ultrasound findings progressed.ConclusionsUsing ultrasound to detect the parotid gland's location before thread lifting might reduce the chance of parotid duct injury. Identifying immediate parotid duct or gland injury with ultrasound can help to act quickly for delayed pain or swelling and reduce the likelihood of additional complications.
Laparoscopic resection of pancreatic masses in 12 dogs
Authors: Poggi Edoardo , Lillo‐Araya Felipe J. , Garcia Rubio David , Pérez Duarte Francisco J. , Gutiérrez del Sol Jorge , Izzo Francesca , Cinti Filippo 
Published: December 2023

AbstractObjectiveTo describe the surgical management and outcome of dogs undergoing laparoscopic pancreatic mass resection (LPMR).Study designRetrospective study.AnimalsTwelve client‐owned dogs.MethodsData collected from medical records of dogs that underwent LPMR between 2012 and 2023 included signalment, clinical signs, mass location within pancreas, preoperative diagnostic imaging, laparoscopic approach, number of portals and device type used for LPMR, operating time, complications and clinical outcome.ResultsPancreatic tumors were located in the left lobe (7), in the right lobe (4) and in the body of the pancreas (1). A 3‐ or 4‐port technique was used in nine and three dogs, respectively. LPMR was performed with the Ligasure in nine dogs, a harmonic scalpel in two dogs and an endoscopic stapler in one dog. The procedure was performed successfully, with no conversion to open laparotomy, in all cases with a median operating time of 69 min. Postoperative complications occurred in four dogs, which resolved with medical treatments. All dogs survived the surgical procedure, were discharged from the hospital and alive a minimum of 90 days postoperatively. The final follow‐up time ranged between 105 and 245 days (median 147). Histopathological diagnosis included insulinoma (9) and pancreatic carcinoma (3).ConclusionLPMR was performed successfully using a 3‐ or 4‐port technique and was associated with a low complication rate and a good clinical outcome.Clinical significanceLPMR may be considered as an alternative to open celiotomy in dogs, particularly for small tumors located in the distal aspect of the pancreatic lobes.
Complete genome sequence of
Heyndrickxia
(
Bacillus
)
coagulans
BC99 isolated from a fecal sample of a healthy infant
Authors: Zhu Mingming , Zhu Jianguo , Fang Shuguang , Zhao Bin 
Published: December 2023

ABSTRACT

This study reports the complete genome sequence of
Heyndrickxia (Bacillus) coagulans
BC99, a promising human probiotic strain isolated from the fecal sample of a healthy infant in Hailaer Inner Mongolia. The genome sequence of BC99 contains a 3,655,496-bp circular chromosome with a GC content of 46.23%. Genome annotation predicted 3,273 protein-coding genes.
Draft genome sequences of five multidrug-resistant
Escherichia coli
strains isolated from vegetable samples in Bangladesh
Authors: Islam Md. Saiful , Pramanik Pritom Kumar , Rana Md. Liton , Ramasamy Srinivasan , Schreinemachers Pepijn , Oliva Ricardo , Rahman Md. Tanvir 
Published: December 2023

ABSTRACT

Reports indicate that vegetables are becoming a source of multidrug-resistant (MDR) bacteria, including
Escherichia coli
. Here, we present genome sequences of five MDR
E. coli
strains to assist future genomic analysis of this bacterium. These
E. coli
strains were isolated from vegetable samples of different gardening systems in Dhaka, Bangladesh.
Structure-based virtual screening and
in vitro
validation of inhibitors of cyclic dinucleotide phosphodiesterases ENPP1 and CdnP
Authors: Rohilla Akshay , Singh Alok Kumar , Koleske Benjamin , Srikrishna Geetha , Bishai William R. 
Published: December 2023

ABSTRACT

Cyclic GMP-AMP synthase (cGAS) and stimulator of interferon genes (STING) are intracellular mediators of innate immune responses to cytosolic pathogen-derived and host DNA. STING agonists designed to mimic the natural host STING ligand, 2′,3′-cyclic GMP-AMP (cGAMP), are promising immunotherapeutic tools for infectious diseases and solid tumor immunotherapy. We previously characterized CdnP (Rv2837c), a specific phosphodiesterase (PDE) deployed by
Mycobacterium tuberculosis
(
M.tb
), as an enzyme that blunts host immunity by directly cleaving bacterial-derived c-di-AMP and host-derived 2′,3′-cGAMP. We hypothesized that small molecule inhibitors of bacterial and host cyclic dinucleotide PDEs, namely CdnP and the endogenous host PDE, ENPP1, might potentiate the STING pathway and act as host-directed therapies (HDTs) for tuberculosis. To this end, we employed virtual screening of an NCI compound library customized for improved oral drug properties to identify potential inhibitors of CdnP and ENPP1. Compounds identified
in silico
were tested for their inhibitory activity against purified CdnP and ENPP1. Using biochemical and cell-based assays, we identified compounds with low IC
50
values against both PDEs. We validated increased cGAS-STING signaling in primary human macrophages exposed to 2′,3′-cGAMP in the presence of a lead ENPP1 inhibitor, E-3 (NCI-14465). Our studies provide a framework for novel HDTs that target the cGAS-STING pathway to promote
M.tb
containment and anti-tumor immunity.

IMPORTANCE

In this paper, we describe novel inhibitors of cyclic dinucleotide phosphodiesterase enzymes from
Mycobacterium tuberculosis
(
M.tb
) (CdnP) and mammals (ENPP1). The phosphodiesterase enzymes hydrolyze cyclic dinucleotides, such as 2′,3′-cyclic GMP-AMP and c-di-AMP, which are stimulator of interferon gene (STING) agonists. By blocking the hydrolysis of STING agonists, the cyclic GMP-AMP synthase (cGAS)-STING-IRF3 pathway is potentiated. There is strong evidence in tuberculosis and in cancer biology that potentiation of the cGAS-STING-IRF3 pathway leads to improved
M.tb
clearance and also improved antitumor responses in cancer. In addition to the identification of novel inhibitors and their biochemical characterization, we provide proof-of-concept evidence that our E-3 inhibitor potentiates the cGAS-STING-IRF3 pathway in both macrophage cell lines and also in primary human monocyte-derived macrophages.
Evaluation of a minimal array of
Treponema pallidum
antigens as biomarkers for syphilis diagnosis, infection staging, and response to treatment
Authors: Haynes Austin M. , Konda Kelika A. , Romeis Emily , Siebert Janet , Vargas Silver K. , Reyes Diaz Michael , Phan Amber , Caceres Carlos F. , Giacani Lorenzo , Klausner Jeffrey D. 
Published: December 2023

ABSTRACT

Syphilis is a multistage chronic sexually transmitted infection caused by the spirochete
Treponema pallidum
subsp.
pallidum
(
T. pallidum
). Today, syphilis is still endemic in low- and middle-income nations and has become resurgent in many high-income countries. Infection can lead to severe sequelae in untreated patients, while vertical transmission of
T. pallidum
is associated with high stillbirth rates and neonatal death. The combination of non-treponemal and treponemal tests allows syphilis serodiagnosis and monitoring of treatment response, albeit not without limitations. In this work, we developed a minimal array for multiple parallel detection of antibodies specific to the immunodominant
T. pallidum
antigens Tp0435 and Tp0574 and 14 additional proteins known to be immunogenic during infection but only partially or not at all evaluated for their diagnostic potential. To assess whether reactivity to these antigens could improve early syphilis diagnosis, serve as biomarkers for disease staging, and monitor response to treatment, we tested the array using 217 serum specimens longitudinally collected pre- and post-treatment from 120 syphilis patients. Results showed significantly different reactivity to a subset of antigens in pre-treatment sera (baseline) when covariates such as syphilis stage, syphilis history, and HIV status were factored in. Furthermore, reactivity to several antigens significantly decreased in post-treatment sera compared to baseline. Although studies with larger sample panels will be needed to validate these findings, this study supports the screening of
T. pallidum
proteomic arrays to identify antigens that could serve as predictors of response and antigens that could help with early syphilis diagnosis.

IMPORTANCE
This manuscript explores the host humoral response to selected antigens of the syphilis agent during infection to evaluate their potential use as diagnostic tests and markers for treatment.
Expanding the microbiologist toolbox
via
new far-red-emitting dyes suitable for bacterial imaging
Authors: Lucidi Massimiliano , Capecchi Giulia , Visaggio Daniela , Gasperi Tecla , Parisi Miranda , Cincotti Gabriella , Rampioni Giordano , Visca Paolo , Kolmakov Kirill 
Published: December 2023

ABSTRACT

Our understanding of bacteria is increasingly dependent on our ability to visualize cellular processes at the single-cell level with high spatial and temporal resolution. Advances in fluorescence microscopy are accompanied by an increasing demand for novel fluorophores that enable tagging specific bacterial components. In this context, new fluorescent probes emitting in the far-red (FR) are of particular interest as they reduce possible interference caused by sample autofluorescence and increase flexibility in multicolor imaging experiments. In this study, an extended set of previously reported and newly synthesized FR-emitting dyes has been characterized for their applicability in live single-cell imaging of the Gram-negative and Gram-positive prototype bacteria
Escherichia coli
and
Bacillus subtilis
. Toxicity tests demonstrated that these dyes do not interfere with the growth kinetics of both species, opening up the possibility of using them in live-cell imaging. Moreover, confocal laser-scanning microscopy imaging revealed that all the tested dyes can distinguish viable from dead bacterial cells. Among the newly synthesized fluorophores, the oxazine derivative KK 1905-NHS was particularly efficient in membrane staining and was effectively employed to monitor membrane biogenesis using a two-step labeling protocol on living cells. In addition, KK 1905-NHS was successfully used in super-resolution stimulated emission depletion microscopy. Overall, the new fluorophores presented in this study expand the microscopy toolbox, which is an asset for the investigation of fundamental bacterial processes.

IMPORTANCE

By harnessing the versatility of fluorescence microscopy and super-resolution imaging, bacteriologists explore critical aspects of bacterial physiology and resolve bacterial structures sized beyond the light diffraction limit. These techniques are based on fluorophores with profitable photochemical and tagging properties. The paucity of available far-red (FR)-emitting dyes for bacterial imaging strongly limits the multicolor choice of bacteriologists, hindering the possibility of labeling multiple structures in a single experiment. The set of FR fluorophores characterized in this study expands the palette of dyes useful for microbiologists, as they can be used for bacterial LIVE/DEAD staining and for tagging the membranes of viable
Escherichia coli
and
Bacillus subtilis
cells. The absence of toxicity makes these dyes suitable for live-cell imaging and allows monitoring of bacterial membrane biogenesis. Moreover, a newly synthesized FR-fluorophore can be employed for imaging bacterial membranes with stimulated emission depletion microscopy, a super-resolution technique capable of increasing the resolving power of conventional microscopes.
Projecting complete redaction of clinical trial protocols (RAPTURE): redacted cross sectional study
Authors: Balaban Nir , Mohyuddin Ghulam Rehman , Kashi Adi , Massarweh Amir , Markel Gal , Bomze David , Goldstein Daniel A , Meirson Tomer 
Published: December 2023

Abstract

Objectives
To characterise redactions in clinical trials and estimate a time when all protocols are fully removed (RAPTURE).

Design
Redacted cross sectional study.

Setting
Published phase 3 randomised controlled trials from 1 January 2010 to ██████████████.

Participants

New England Journal of Medicine
, █
█████████
, and
Journal of the American Medical Association
.

Main outcome measures
█████ ████████ ██████████████ ██████ ██████████ ████████ ████████ ██████████ ███████████ ████████████ ████████████ ████████████████████████ ██████████████████

Results
████████████████████ met the inclusion criteria, with 268 (56.7%) research protocols available and accessible. The rate of redactions in protocols has increased from 0 in 2010 to 60.8% in 2021 (P<0.001). The degree of data redaction has also increased, with the average cumulative redactions among industry funded trials rising from 0 in 2010 to 3.5 pages in 2021 (P<0.001). Modelling predicts that RAPTURE is expected to occur between 2073 and 2136. Redactions featured predominantly in ████████ sponsored trials and mostly occurred in the statistical design.

Conclusions
This study highlights the rise in protocol redactions and predicts that, ██████████████████████████████████████████ will be entirely redacted between 2073 and 2136. A legitimate rationale for the redactions could ███ be found. A multipronged strategy against protocol redactions is required to maintain the integrity of science.

Availability
This paper is partially redacted, but for the sake of ███████████, a version without any redactions can be found in the supplementary material.
Knowledge and practice of nurses with respect to perioperative hypothermia prevention in the Northwest Amhara Regional State Referral Hospitals, Ethiopia: a cross-sectional study
Authors: Woretaw Ashenafi Worku , Yimer Mekonnen Bezenaw , Tsegaye Netsanet , Dellie Endalkachew 
Published: December 2023

ObjectivesIt has been reported that maintaining a normal body temperature among surgical patients can reduce the length of hospitalisation by up to 40%, decrease the risk of surgical site infection by 64% and reduce mortality by fourfold. Nurses are primarily responsible for preventing the occurrence of hypothermia among surgical patients. This study assessed nurses’ knowledge and practices with respect to perioperative hypothermia prevention in Northwest Ethiopia, and investigated the factors associated with good knowledge and practice.DesignCross-sectional study.SettingNorthwest Amhara Regional State Referral Hospitals, Northwest Ethiopia, 25 March–20 May 2021.Participants413 nurses working in the perioperative units of five referral hospitals.Outcome measuresPerioperative hypothermia prevention knowledge and practice among nurses.ResultsNearly three-fifths (59.1%; 95% CI: 54.7% to 63.7%) of respondents had good knowledge and about half (50.4%; 95% CI: 45.5% to 55.0%) had good practice with respect to perioperative hypothermia prevention. Factors associated with nurses’ knowledge of prevention of perioperative hypothermia included male sex (adjusted OR (AOR): 1.61, 95% CI: 1.02 to 2.53), having a bachelor’s degree (AOR: 2.50, 95% CI: 1.25 to 5.00), having a master’s degree (AOR: 4.39, 95% CI: 1.45 to 13.20) and training participation (AOR: 3.68, 95% CI: 2.14 to 6.33). Factors associated with nurses’ practice of prevention of perioperative hypothermia included working in recovery (AOR: 2.87, 95% CI: 1.08 to 7.58) and intensive care units (AOR: 2.39, 95% CI: 1.09 to 5.22), training participation (AOR: 2.64, 95% CI: 1.53 to 4.57), being satisfied with their job (AOR: 2.15, 95% CI: 1.34 to 3.43) and having good knowledge (AOR: 2.64, 95% CI: 1.63 to 4.27).ConclusionNurses’ knowledge and practice of the prevention of perioperative hypothermia were inadequate. Hospital managers need to design and strengthen training programmes and work to enhance job satisfaction.
Effectiveness, safety and costs of the FreeStyle Libre glucose monitoring system for children and adolescents with type 1 diabetes in Spain: a prospective, uncontrolled, pre-post study
Authors: González-Pacheco Himar , Rivero-Santana Amado , Ramallo-Fariña Yolanda , Valcárcel-Nazco Cristina , Álvarez-Pérez Yolanda , García-Pérez Lidia , García-Bello Miguel Angel , Perestelo-Pérez Lilisbeth , Serrano-Aguilar Pedro 
Published: December 2023

ObjectivesThis study aimed to evaluate the effectiveness, safety and costs of FreeStyle Libre (FSL) glucose monitoring system for children and adolescents with type 1 diabetes mellitus (T1DM) in Spain.DesignProspective, multicentre pre-post study.SettingThirteen Spanish public hospitals recruited patients from January 2019 to March 2020, with a 12-month follow-up.Participants156 patients were included.Primary and secondary outcome measuresPrimary: glycated haemoglobin (HbA1c) change. Secondary: severe hypoglycaemic events (self-reported and clinical records), quality of life, diabetes treatment knowledge, treatment satisfaction, adverse events, adherence, sensor usage time and scans. Healthcare resource utilisation was assessed for cost analysis from the National Health System perspective, incorporating direct healthcare costs. Data analysis used mixed regression models with repeated measures. The intervention’s total cost was estimated by multiplying health resource usage with unit costs.ResultsIn the whole sample, HbA1c increased significantly (0.32%; 95% CI 0.10% to 0.55%). In the subgroup with baseline HbA1c≥7.5% (n=88), there was a significant reduction at 3 months (−0.46%; 95% CI −0.69% to −0.23%), 6 months (−0.49%; 95% CI −0.73% to −0.25%) and 12 months (−0.43%; 95% CI −0.68% to –0.19%). Well-controlled patients had a significant 12-month worsening (0.32%; 95% CI 0.18% to 0.47%). Self-reported severe hypoglycaemia significantly decreased compared with the previous year for the whole sample (−0.37; 95% CI −0.62 to –0.11). Quality of life and diabetes treatment knowledge showed no significant differences, but satisfaction increased. Adolescents had lower sensor usage time and scans than children. Reduction in HbA1c was significantly associated with device adherence. No serious adverse effects were observed. Data suggest that use of FSL could reduce healthcare resource use (strips and lancets) and costs related to productivity loss.ConclusionsThe use of FSL in young patients with T1DM was associated with a significant reduction in severe hypoglycaemia, and improved HbA1c levels were seen in patients with poor baseline control. Findings suggest cost savings and productivity gains for caregivers. Causal evidence is limited due to the study design. Further research is needed to confirm results and assess risks, especially for patients with lower baseline HbA1c.