bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drivers and determinants of strain dynamics following fecal microbiota transplantation
Authors: Schmidt Thomas S. B. , Li Simone S. , Maistrenko Oleksandr M. , Akanni Wasiu , Coelho Luis Pedro , Dolai Sibasish , Fullam Anthony , Glazek Anna M. , Hercog Rajna , Herrema Hilde , Jung Ferris , Kandels Stefanie , Orakov Askarbek , Thielemann Roman , von Stetten Moritz , Van Rossum Thea , Benes Vladimir , Borody Thomas J. , de Vos Willem M. , Ponsioen Cyriel Y. , Nieuwdorp Max , Bork Peer 
Published: September 2022

AbstractFecal microbiota transplantation (FMT) is a therapeutic intervention for inflammatory diseases of the gastrointestinal tract, but its clinical mode of action and subsequent microbiome dynamics remain poorly understood. Here we analyzed metagenomes from 316 FMTs, sampled pre and post intervention, for the treatment of ten different disease indications. We quantified strain-level dynamics of 1,089 microbial species, complemented by 47,548 newly constructed metagenome-assembled genomes. Donor strain colonization and recipient strain resilience were mostly independent of clinical outcomes, but accurately predictable using LASSO-regularized regression models that accounted for host, microbiome and procedural variables. Recipient factors and donor–recipient complementarity, encompassing entire microbial communities to individual strains, were the main determinants of strain population dynamics, providing insights into the underlying processes that shape the post-FMT gut microbiome. Applying an ecology-based framework to our findings indicated parameters that may inform the development of more effective, targeted microbiome therapies in the future, and suggested how patient stratification can be used to enhance donor microbiota colonization or the displacement of recipient microbes in clinical practice.
Repeated exposure to either consistently spatiotemporally congruent or consistently incongruent audiovisual stimuli modulates the audiovisual common-cause prior
Authors: Hong Fangfang , Badde Stephanie , Landy Michael S. 
Published: September 2022

AbstractTo estimate an environmental property such as object location from multiple sensory signals, the brain must infer their causal relationship. Only information originating from the same source should be integrated. This inference relies on the characteristics of the measurements, the information the sensory modalities provide on a given trial, as well as on a cross-modal common-cause prior: accumulated knowledge about the probability that cross-modal measurements originate from the same source. We examined the plasticity of this cross-modal common-cause prior. In a learning phase, participants were exposed to a series of audiovisual stimuli that were either consistently spatiotemporally congruent or consistently incongruent; participants’ audiovisual spatial integration was measured before and after this exposure. We fitted several Bayesian causal-inference models to the data; the models differed in the plasticity of the common-source prior. Model comparison revealed that, for the majority of the participants, the common-cause prior changed during the learning phase. Our findings reveal that short periods of exposure to audiovisual stimuli with a consistent causal relationship can modify the common-cause prior. In accordance with previous studies, both exposure conditions could either strengthen or weaken the common-cause prior at the participant level. Simulations imply that the direction of the prior-update might be mediated by the degree of sensory noise, the variability of the measurements of the same signal across trials, during the learning phase.
Adjunctive therapy with the Tie2 agonist Vasculotide reduces pulmonary permeability in Streptococcus pneumoniae infected and mechanically ventilated mice
Authors: Lask Aina , Gutbier Birgitt , Kershaw Olivia , Nouailles Geraldine , Gruber Achim D. , Müller-Redetzky Holger C. , Chackowicz Steven , Hamilton Douglas A. , Van Slyke Paul , Witzenrath Martin 
Published: September 2022

AbstractCommunity acquired pneumonia, mainly caused by Streptococcus pneumoniae (S.pn.), is a common cause of death worldwide. Despite adequate antibiotic therapy, pneumococcal pneumonia can induce pulmonary endothelial hyperpermeability leading to acute lung injury, which often requires mechanical ventilation (MV) causing ventilator-induced lung injury (VILI). Endothelial stabilization is mediated by angiopoietin-1 induced Tie2 activation. PEGylated (polyethylene glycol) Tie2-agonist Vasculotide (VT) mimics Angiopietin-1 effects. Recently, VT has been shown to reduce pulmonary hyperpermeability in murine pneumococcal pneumonia. The aim of this study was to determine whether VT reduces lung damage in S.pn. infected and mechanically ventilated mice. Pulmonary hyperpermeability, immune response and bacterial load were quantified in S.pn. infected mice treated with Ampicillin + /−VT and undergoing six hours of MV 24 h post infection. Histopathological lung changes, Tie2-expression and -phosphorylation were evaluated. VT did not alter immune response or bacterial burden, but interestingly combination treatment with ampicillin significantly reduced pulmonary hyperpermeability, histological lung damage and edema formation. Tie2-mRNA expression was reduced by S.pn. infection and/or MV but not restored by VT. Moreover, Tie2 phosphorylation was not affected by VT. These findings indicate that VT may be a promising adjunctive treatment option for prevention of VILI in severe pneumococcal pneumonia.
The influence of the rotational speed of the meat cutter knives and bowl on the microstructure of meat products
Authors: Krzywdzińska-Bartkowiak Mirosława , Piątek Michał , Kowalski Ryszard 
Published: September 2022

AbstractThe aim of the study was to determine the structure of meat batter and processed meat products, depending on the chopping time and rotational speed of the cutter knives and bowl, by means of histochemical methods combined with the computer image analysis system. Finely comminuted meat batters and processed meat products were investigated. Four variants of the rotational speed of cutter knives and bowl were applied in the experiment: 1500/10 rpm, 1500/20 rpm , 3000/10 rpm and 3000/20 rpm. The chopping process lasted 10 min. After 5, 6, 8 and 10 min of chopping samples of meat batter and processed meat products were collected for histological analyses. The microstructure of structural elements (fat globules and collagen fibres) was measured using computer image analysis. The following parameters were included in a characteristic of the images: the area, circumference, length and width of fat fields; the number of fat fields analysed; the percentage of fat fields in the field under analysis; the area, circumference, length and width of collagen fibres. The computer image analysis showed that the optimal speed of the cutter knives and bowl was 3000/20 rpm. The chopping time was reduced from 10 to 8 min.
Road damage detection algorithm for improved YOLOv5
Authors: Guo Gege , Zhang Zhenyu 
Published: September 2022

AbstractRoad damage detection is an important task to ensure road safety and realize the timely repair of road damage. The previous manual detection methods are low in efficiency and high in cost. To solve this problem, an improved YOLOv5 road damage detection algorithm, MN-YOLOv5, was proposed. We optimized the YOLOv5s model and chose a new backbone feature extraction network MobileNetV3 to replace the basic network of YOLOv5, which greatly reduced the number of parameters and GFLOPs of the model, and reduced the size of the model. At the same time, the coordinate attention lightweight attention module is introduced to help the network locate the target more accurately and improve the target detection accuracy. The KMeans clustering algorithm is used to filter the prior frame to make it more suitable for the dataset and to improve the detection accuracy. To improve the generalization ability of the model, a label smoothing algorithm is introduced. In addition, the structure reparameterization method is used to accelerate model reasoning. The experimental results show that the improved YOLOv5 model proposed in this paper can effectively identify pavement cracks. Compared with the original model, the mAP increased by 2.5%, the F1 score increased by 2.6%, and the model volume was smaller than that of YOLOv5. 1.62 times, the parameter was reduced by 1.66 times, and the GFLOPs were reduced by 1.69 times. This method can provide a reference for the automatic detection method of pavement cracks.
Orphan drug development in alpha-1 antitypsin deficiency
Authors: Trudzinski Franziska C. , Presotto Maria Ada , Buck Emanuel , Herth Felix J. F. , Ries Markus 
Published: September 2022

AbstractAlpha-1 antitrypsin deficiency (AATD, OMIM #613490) is a rare metabolic disorder affecting lungs and liver. The purpose of this study is to assess the impact of the US orphan drug act on AATD by providing a quantitative clinical-regulatory insight into the status of FDA orphan drug approvals and designations for compounds intended to treat AATD. This is across-sectional analysis of the FDA database for orphan drug designations. Primary endpoint: orphan drug approvals. Secondary endpoint: orphan drug designations by the FDA. Close of database was 16 July 2021. STROBE criteria were respected. Primary outcome: one compound, alpha-1-proteinase inhibitor (human) was approved as an orphan drug in 1987 with market exclusivity until 1994. Secondary outcome: sixteen compounds received FDA orphan drug designation including protein, anti-inflammatory, mucolytic, gene, or cell therapy. Drug development activities in AATD were comparable to other rare conditions and led to the FDA-approval of one compound, based on a relatively simple technological platform. The current unmet medical need to be addressed are extrapulmonary manifestations, in this case the AATD-associated liver disease. Orphan drug development is actually focusing on (1) diversified recombinant AAT production platforms, and (2) innovative gene therapies, which may encompass a more holistic therapeutic approach.
Deciphering the therapeutical potentials of rosmarinic acid
Authors: El Kantar Sally , Yassin Ali , Nehmeh Bilal , Labaki Louis , Mitri Sara , Naser Aldine Fatima , Hirko Aaron , Caballero Sergio , Monck Eileen , Garcia-Maruniak Alejandra , Akoury Elias 
Published: September 2022

AbstractLemon balm is herbal tea used for soothing stomach cramps, indigestion, and nausea. Rosmarinic acid (RA) is one of its chemical constituents known for its therapeutic potentials against cancer, inflammatory and neuronal diseases such as the treatment of neurofibromatosis or prevention from Alzheimer’s diseases (AD). Despite efforts, recovery and purification of RA in high yields has not been entirely successful. Here, we report its aqueous extraction with optimal conditions and decipher the structure by nuclear magnetic resonance (NMR) spectroscopy. Using various physical–chemical and biological assays, we highlight its anti-aggregation inhibition potentials against the formation of Tau filaments, one of the hallmarks of AD. We then examine its anti-cancer potentials through reduction of the mitochondrial reductase activity in tumor cells and investigate its electrochemical properties by cyclic voltammetry. Our data demonstrates that RA is a prominent biologically active natural product with therapeutic potentials for drug discovery in AD, cancer therapy and inflammatory diseases.
Unbiased approach to identify and assess efficacy of human SARS-CoV-2 neutralizing antibodies
Authors: Cao Xia , Maruyama Junki , Zhou Heyue , Fu Yanwen , Kerwin Lisa , Powers Colin , Sattler Rachel A. , Manning John T. , Singh Alok , Lim Reyna , Healy Laura D. , Johnson Sachi , Paz Cabral Elizabeth , Li Donghui , Lu Lucy , Ledesma Arthur , Lee Daniel , Richards Susan , Rivero-Nava Laura , Li Yan , Shen Weiqun , Stegman Karen , Blair Benjamin , Urata Shinji , Kishimoto-Urata Magumi , Ko Jamie , Du Na , Morais Kyndal , Lawrence Kate , Rivera Ianne , Pai Chin-I. , Bresson Damien , Brunswick Mark , Zhang Yanliang , Ji Henry , Paessler Slobodan , Allen Robert D. 
Published: September 2022

AbstractCoronavirus disease 2019 (COVID-19) continues to significantly impact the global population, thus countermeasure platforms that enable rapid development of therapeutics against variants of SARS-CoV-2 are essential. We report use of a phage display human antibody library approach to rapidly identify neutralizing antibodies (nAbs) against SARS-CoV-2. We demonstrate the binding and neutralization capability of two nAbs, STI-2020 and STI-5041, against the SARS-CoV-2 WA-1 strain as well as the Alpha and Beta variants. STI-2020 and STI-5041 were protective when administered intravenously or intranasally in the golden (Syrian) hamster model of COVID-19 challenged with the WA-1 strain or Beta variant. The ability to administer nAbs intravenously and intranasally may have important therapeutic implications and Phase 1 healthy subjects clinical trials are ongoing.
Transcriptomic analysis of Staphylococcus equorum KM1031 from the high-salt fermented seafood jeotgal under chloramphenicol, erythromycin and lincomycin stresses
Authors: Heo Sojeong , Kim Tao , Na Hong-Eun , Lee Gawon , Lee Jong-Hoon , Jeong Do-Won 
Published: September 2022

AbstractStaphylococcus equorum strain KM1031 is resistant to chloramphenicol, erythromycin and lincomycin. To shed light on the genetic factors underlying these antibiotic resistances, we determined the global gene expression profile of S. equorum KM1031 using RNA sequencing. During chloramphenicol, erythromycin and lincomycin treatment, 8.3% (183/2,336), 16.0% (354/2,336), and 2.9% (63/2,336) of S. equorum KM1031 genes exhibited significant differences in expression, respectively. These three antibiotics upregulated genes related to efflux and downregulated genes related to transporters. Antibiotic treatment also upregulated osmoprotectant-related genes involved in salt tolerance. To identify specific genes functionally related to antibiotic resistance, we compared the genome of strain KM1031 with those of three S. equorum strains that are sensitive to these three antibiotics. We identified three genes of particular interest: an antibiotic biosynthesis monooxygenase gene (abm, AWC34_RS01805) related to chloramphenicol resistance, an antibiotic ABC transporter ATP-binding protein gene (msr, AWC34_RS11115) related to erythromycin resistance, and a lincosamide nucleotydyltransferase gene (lnuA, AWC34_RS13300) related to lincomycin resistance. These genes were upregulated in response to the corresponding antibiotic; in particular, msr was upregulated more than fourfold by erythromycin treatment. Finally, the results of RNA sequencing were validated by quantitative real-time PCR. This transcriptomic analysis provides genetic evidence regarding antibiotic stress responses of S. equorum strain KM1031.
Umsetzung von Tabakkontrollmaßnahmen in Einrichtungen der
Kinder- und Jugendpsychiatrie: Eine Online-Befragung von leitenden
Mitarbeitenden
Authors: Kuitunen-Paul Sören , Teichmann Marko , Mühlig Stephan , Lochbühler Kirsten , Roessner Veit , Rustler Christa , Rüther Tobias , Smolka Michael N. , Rabenstein Andrea 
Published: September 2022

Zusammenfassung
Ziel der Studie Tabakkontrollmaßnahmen sind auch in kinder- und
jugendpsychiatrischen (KJP) Einrichtungen relevant. Ihre Umsetzung in deutschen
KJP-Einrichtungen soll erfragt werden.
Methodik In einer Online-Studie beantworteten n=78
Klinikdirektorinnen/Klinikdirektoren und leitende Mitarbeitende Fragen
zum stationsübergreifenden sowie stationsspezifischen Umgang mit
rauchenden Patientinnen und Patienten.
Ergebnisse Zahlreiche Einrichtungen (70–87%) haben
Rauchverbote für Jugendliche in Gebäuden und Gelände. Je
nach Stationstyp werden aber Ausnahmen gemacht, z. B. in Raucherzonen
(38%), Raucherpavillons (19%) oder für Kinder und
Jugendliche mit bestimmten Störungsbildern (28%).
Regelverstöße werden je nach Stationstyp unterschiedlich
häufig dokumentiert (30–79%), führen aber
regelmäßig zu Konsequenzen (84–93%) wie
Tabakeinbehalt (42–63%) oder Ausgangsbeschränkungen
(25–38%). Unterstützende
Tabakentwöhnungsangebote bestehen in 78% der Kliniken, vor allem
in Form von Einzelberatung (64%). Eine pharmakologische Behandlung wird
vor allem stationär genutzt (71–83%). Jede zweite
Einrichtung berichtet von Ergebniskontrollen nach Tabakentwöhnung
(54%), während von Arbeitskreisen (14%) und der
Anwendung standardisierter Diagnoseinstrumente (0–4%) seltener
berichtet wird.
Diskussion Damit liegen erstmals deutschlandweite Daten zur Tabakkontrolle
in KJP-Einrichtungen vor, aus denen sich zukünftige Handlungsfelder
für die Tabakkontrolle ableiten lassen.
Tripartite Motif Containing 26 is a Positive Predictor for
Endometrial Carcinoma Patients and Regulates Cell Survival in Endometrial
Carcinoma
Authors: Lu Tanmin , Wu Yu 
Published: September 2022

AbstractFunctioning as an E3 ubiquitin ligase, tripartite motif containing 26 (TRIM26)
can regulate the tumor behavior and the relevant inflammatory immune response.
Endometrial carcinoma is a major gynecological malignant tumor in the world,
while no relevant research has been performed. KMplot, a web-based survival
analysis tool, demonstrated that TRIM26 expression was positively correlated
with the overall survival in gynecological tumors, such as ovarian, cervical,
and endometrial cancer. The relatively low expression of TRIM26 was also found
in endometrial cancer tissues and endometrial cancer cell lines. In the online
Gene Expression Profiling Interactive Analysis (GEPIA) platform, TRIM26 was
positively correlated with the pre-apoptosis genes of p53, BIM, BID, BAX, and
BAK, and negatively correlated with the anti-apoptosis gene of BCLW. To further
explore the function of TRIM26 in endometrial carcinoma, Ishikawa and KLE cells
were infected with PLVX-TRIM26-derived lentivirus. TRIM26 overexpression
suppressed the growth of endometrial cells, with downregulated p-AKT and
upregulated BIM and BID expression. PLVX-TRIM26 overexpressed Ishikawa cells
were injected subcutaneously into the side flanks of male BALB/C nude
mice to construct a TRIM26-overexpression xenograft model. TRIM26 overexpression
suppressed the growth of endometrial cancer as indicated by downregulated tumor
volume and tumor weight with downregulated p-AKT expression. TRIM26 could
regulate AKT pathway and apoptosis process to inhibit the growth of endometrial
carcinoma, which can be utilized as a survival predictor.
Visible-Light-Induced Aerobic Oxidation of Tertiary Silanes to Silanols using Molecular Oxygen as an Oxidant
Authors: He Pei , Zhang Fengmei , Tang Shiyun , Gui Qing-Wen , Si Xiaoxi , Jiang Wei , Shen Qinpeng , Li Zhenjie , Zhu Zhiyang 
Published: September 2022

AbstractThe photocatalyzed synthesis of silanols from tertiary si­lanes has been carried out using eosin Y under air. This is a metal-free method that uses a low catalyst loading, atmospheric oxygen as the oxidant, and visible-light conditions (blue light).
Phosphofurin Acidic Cluster Sorting Protein 1 Syndrome: Insights Gained on the Multisystem Involvement Reviewing Encoded Protein Interactions?
Authors: Thakur Seema , Paliwal Preeti , Farmania Rajni , Khandelwal Vipin , Garg Vivek 
Published: September 2022

AbstractMutations in PACS1 cause moderate-to-severe intellectual disability. Very few cases of PACS1 neurodevelopment disorder have been described in the literature that were identified using whole exome sequencing (WES). We report a case of de novo PACS1 mutation identified through WES after an initial workup for mucopolysaccharidosis. Through this case, we wish to emphasize that most important clinical clue in the facial gestalt is a downturned angle of mouth, thin lips, and wide mouth, giving characteristic wavy appearance of face that can distinguish these cases and can prevent unnecessary workup for the patients.
Quantifying the Electronic Health Record Burden in Head and Neck Cancer Care
Authors: Ebbers Tom , Kool Rudolf B. , Smeele Ludi E. , Takes Robert P. , van den Broek Guido B. , Dirven Richard 
Published: September 2022

Abstract
Background Although the main task of health care providers is to provide patient care, studies show that increasing amounts of time are spent on documentation.
Objective To quantify the time and effort spent on the electronic health record (EHR) in head and neck cancer care.
Methods Cross-sectional time–motion study. Primary outcomes were the percentages of time spent on the EHR and the three main tasks (chart review, input, placing orders), number of mouse events, and keystrokes per consultation. Secondary outcome measures were perceptions of health care providers regarding EHR documentation and satisfaction.
Results In total, 44.0% of initial oncological consultation (IOC) duration and 30.7% of follow-up consultation (FUC) duration are spent on EHR tasks. During 80.0% of an IOC and 67.9% of a FUC, the patient and provider were actively communicating. Providers required 593 mouse events and 1,664 keystrokes per IOC and 140 mouse events and 597 keystrokes per FUC, indicating almost 13 mouse clicks and close to 40 keystrokes for every minute of consultation time. Less than a quarter of providers indicated that there is enough time for documentation.
Conclusion This study quantifies the widespread concern of high documentation burden for health care providers in oncology, which has been related to burnout and a decrease of patient–clinician interaction. Despite excessive time and effort spent on the EHR, health care providers still felt this was insufficient for proper documentation. However, the need for accurate and complete documentation is high, as reuse of information becomes increasingly important. The challenge is to decrease the documentation burden while increasing the quality of EHR data.
Identification of tourists’ dynamic risk perception—the situation in Tibet
Authors: Feng Yuyao , Li Guowen , Sun Xiaolei , Li Jianping 
Published: September 2022

AbstractThis paper proposes an identification framework for dynamic risk perception with “Questions & Answers (Q&As) + travel notes”, which newly attends to the dynamic nature of risk perception and overcomes the liabilities of traditional data collection methods, such as questionnaires and interviews, which induce high costs in data acquisition, tend to produce small sample sizes and suffer from large sample deviations. Via 2627 Q&As released by tourists before travel and 17,523 travel notes released by tourists after travel, the dynamic change in 20 identified risks before and after travel to Tibet is portrayed with the help of text mining technologies, which can automatically identify risk perception types and sentiment tendencies from massive amounts of textual data. The study finds that before travel, tourists usually underestimate risks related to safety, health and time but overestimate risks related to transportation, route selection and season. The results of the study are not only informative for destination tourism risk management and image promotion but also important for tourists to form more reasonable risk assessments.
A frequency comb stabilized Ti:Sa laser as a self-reference for ion-trap experiments with a 40Ca+ ion
Authors: Domínguez F. , Bañuelos J. , Berrocal J. , del Pozo J. J. , Hernández M. , Carrasco-Sanz A. , Cerrillo J. , Escobedo-Araque P. , Rodríguez D. 
Published: September 2022

In this study, we report on the stabilization of a continuous-wave Ti:Sa laser to an optical frequency comb. The laser is emitting at 866 nm to address one of the transitions required for Doppler cooling of a single 40Ca+ ion in a linear Paul trap (2D3/2↔P1/22). The stabilized Ti:Sa laser is utilized to calibrate an ultra-accurate wavelength meter. We certify this self-reference laser source by comparing the results from monitoring the laser-cooled 40Ca+ ion in the linear Paul trap, with those obtained when a HeNe laser is used for calibration. The use of this self-reference is compatible with the simultaneous use of the comb for precision spectroscopy in the same ion-trap experiment.