bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic responses of plasma to extreme environments in overwintering Tibetan frogs Nanorana parkeri: a metabolome integrated analysis
Authors: Niu Yonggang , Zhang Xuejing , Zhang Haiying , Xu Tisen , Zhu Lifeng , Storey Kenneth B. , Chen Qiang 
Published: August 2021

AbstractMany animals lower their metabolic rate in response to low temperatures and scarcity of food in the winter in phenomena called hibernation or overwintering. Living at high altitude on the Tibetan Plateau where winters are very cold, the frogNanorana parkeri, survives in one of the most hostile environments on Earth but, to date, relatively little is known about the biochemical and physiological adjustments for overwintering by this species. The present study profiled changes in plasma metabolites ofN. parkeribetween winter and summer using UHPLC-QE-MS non-target metabolomics in order to explore metabolic adaptations that support winter survival. The analysis showed that, in total, 11 metabolites accumulated and 95 were reduced in overwintering frogs compared with summer-active animals. Metabolites that increased included some that may have antioxidant functions (canthaxanthin, galactinol), act as a metabolic inhibitor (mono-ethylhexylphthalate), or accumulate as a product of anaerobic metabolism (lactate). Most other metabolites in plasma showed reduced levels in winter and were generally involved in energy metabolism including 11 amino acids (proline, isoleucine, leucine, valine, phenylalanine, tyrosine, arginine, tryptophan, methionine, threonine and histidine) and 4 carbohydrates (glucose, citrate, succinate, and malate). Pathway analysis indicated that aminoacyl-tRNA biosynthesis, phenylalanine, tyrosine and tryptophan biosynthesis, and nitrogen metabolism were potentially the most prominently altered pathways in overwintering frogs. Changes to these pathways are likely due to fasting and global metabolic depression in overwintering frogs. Concentrations of glucose and urea, commonly used as cryoprotectants by amphibians that winter on land, were significantly reduced during underwater hibernation inN. parkeri. In conclusion, winter survival of the high-altitude frog,N. parkeriwas accompanied by substantial changes in metabolomic profiles and this study provides valuable information towards understanding the special adaptive mechanisms ofN. parkerito winter stresses.
Development of a method for evaluating the mRNA transcription activity of influenza virus RNA-dependent RNA polymerase through real-time reverse transcription polymerase chain reaction
Authors: Horio Yuka , Shichiri Mototada , Isegawa Yuji 
Published: August 2021

Abstract
Background
The development of an influenza RNA-dependent RNA polymerase (RdRp) inhibitor is required; therefore, a method for evaluating the activity of influenza RdRp needs to be developed. The current method uses an ultracentrifuge to separate viral particles and quantifies RdRp activity with radioisotope-labeled nucleosides, such as 32P-GTP. This method requires special equipment and radioisotope management, so it cannot be implemented in all institutions. We have developed a method to evaluate the mRNA transcription activity of RdRp without using ultracentrifugation and radioisotopes.

Results
RdRp was extracted from viral particles that were purified from the culture supernatant using anionic polymer-coated magnetic beads that can concentrate influenza virus particles from the culture supernatant in approximately 30 min. A strand-specific real-time reverse transcription polymerase chain reaction (RT-PCR) method was developed based on reverse transcription using tagged primers. RT primers were designed to bind to a sequence near the 3' end of mRNA containing a poly A tail for specific recognition of the mRNA, with an 18-nucleotide tag attached to the 5' end of the sequence. The RT reaction was performed with this tagged RT primer, and the amount of mRNA was analyzed using real-time qPCR. Real-time qPCR using the tag sequence as the forward primer and a segment-specific reverse primer ensured the specificity for quantifying the mRNA of segments 1, 4, and 5. The temperature, reaction time, and Mg2+ concentration were determined to select the optimum conditions for in vitro RNA synthesis by RdRp, and the amount of synthesized mRNAs of segments 1, 4, and 5 was determined with a detection sensitivity of 10 copies/reaction. In addition, mRNA synthesis was inhibited by ribavirin triphosphate, an RdRp inhibitor, thus indicating the usefulness of this evaluation method for screening RdRp inhibitors.

Conclusion
This method makes it possible to analyze the RdRp activity even in a laboratory where ultracentrifugation and radioisotopes cannot be used. This novel method for measuring influenza virus polymerase activity will further promote research to identify compounds that inhibit viral mRNA transcription activity of RdRp.
Resistance induction based on the understanding of molecular interactions between plant viruses and host plants
Authors: Akhter Md. Shamim , Nakahara Kenji S. , Masuta Chikara 
Published: August 2021

Abstract
Background
Viral diseases cause significant damage to crop yield and quality. While fungi- and bacteria-induced diseases can be controlled by pesticides, no effective approaches are available to control viruses with chemicals as they use the cellular functions of their host for their infection cycle. The conventional method of viral disease control is to use the inherent resistance of plants through breeding. However, the genetic sources of viral resistance are often limited. Recently, genome editing technology enabled the publication of multiple attempts to artificially induce new resistance types by manipulating host factors necessary for viral infection.

Main body
In this review, we first outline the two major (R gene-mediated and RNA silencing) viral resistance mechanisms in plants. We also explain the phenomenon of mutations of host factors to function as recessive resistance genes, taking the eIF4E genes as examples. We then focus on a new type of virus resistance that has been repeatedly reported recently due to the widespread use of genome editing technology in plants, facilitating the specific knockdown of host factors. Here, we show that (1) an in-frame mutation of host factors necessary to confer viral resistance, sometimes resulting in resistance to different viruses and that (2) certain host factors exhibit antiviral resistance and viral-supporting (proviral) properties.

Conclusion
A detailed understanding of the host factor functions would enable the development of strategies for the induction of a new type of viral resistance, taking into account the provision of a broad resistance spectrum and the suppression of the appearance of resistance-breaking strains.
One-week recall period gives a more accurate estimate of exclusive breastfeeding practice than 24-h recall among infants younger than six months of age
Authors: Andarge Sewitemariam Desalegn , Fenta Esete Habtemariam , Gebreyesus Seifu Hagos , Belachew Robel Yirgu 
Published: August 2021

Abstract
Background
The World Health Organization recommends a 24-h recall period to estimate breastfeeding practice of mothers of infants aged younger than six-months. Though 24-h recall was preferred for its low recall bias and for practical reasons, it can overestimate exclusive breastfeeding practice (EBF). Validating this indicator will help account for the deviation from the true estimate. This prospective cohort study measured accuracy of the 24-h recall method and validates a week recall as an alternative approach for use in a small sample population.

Method
The study was conducted from March to April 2018 involving 408 mother-infant pairs living in Butajira Health and Demographic Surveillance Site (HDSS), Southern Ethiopia. Participants were prospectively followed for 14 consecutive days; where their breastfeeding practice in the past 24 h was measured daily. Exclusive breastfeeding prevalence estimate obtained using the 24-h recall method and recall periods spanning a varying number of days (short period recalls) was compared against the cumulative of the responses from a prospectively measured repeated 24-h recalls over the course of 14 days. McNemar statistics was used to assess statistical significance of the difference in the EBF prevalence estimates of the single 24-h recall and the reference standard. Sensitivity, specificity, positive predictive value and negative predictive values were calculated to determine the level of accuracy. Receiver Operating Characteristics curve was used to measure the difference in performance between the two methods.

Result
The highest prevalence (71.4%) of exclusive breastfeeding practice was estimated using the single 24-h recall method whereas the lowest breastfeeding practice (47.1%) was obtained from a cumulative of 14 repeated 24-h recalls. A week recall (a recall over 7 days’ period), resulted in the smallest discrepancy in estimate (7.1%) as compared to cumulative estimate of 14 repeated 24-h recalls. Comparing against our reference standard, a week recall had 96.7% sensitivity and 83.5% specificity in estimating exclusive breastfeeding practice.

Conclusions
Using single 24-h recall method overestimated exclusive breastfeeding prevalence. However, a week recall gave an estimate close to the estimate from the standard method. A week recall has a potential to balance the tradeoff between the accuracy of EBF estimates and the resource implication of using multiple prospective measurements that have a proven superior accuracy.
Influence of physician networks on prescribing a new ingredient combination in heart failure: a longitudinal claim data-based study
Authors: Arnold Christine , Koetsenruijter Jan , Forstner Johanna , Peters-Klimm Frank , Wensing Michel 
Published: August 2021

Abstract
Background
Since 2016, the combination of sacubitril/valsartan, which combines an angiotensin receptor and neprilysin inhibitor (ARNI), has been recommended in the guidelines for the treatment of heart failure. The adoption of new drugs may be influenced by collaboration and exchange between physicians. We aimed to determine whether characteristics of the professional networks of prescribing physicians were associated with the prescribing of ARNI in Germany.

Methods
We conducted a longitudinal analysis based on claims data in 2016–2018 in Germany. The characteristics of ambulatory care physicians’ networks were determined in the analysis of the patient-sharing networks of physicians in 2017. Binary logistic regression analysis with the outcome ‘prescribes ARNI in 2018’ (present or absent) was carried out, using network characteristics as predictors, adjusted for specialty and sociodemographic characteristics of physicians.

Results
The network analysis included 8370 physicians, who had 144,636 connections. Prescribers had more connections to other physicians compared to non-prescribers (median 31 vs. 23). Regression analysis showed that the numbers of linkages to prescribers of ARNI were positively associated with prescribing ARNI. For 6–10 connections, the average marginal effect (AME) was 0.04 (confidence interval [CI] 95% 0.01–0.06) and for > 10 links the AME 0.07 (CI 95% 0.05–0.10) compared to 0–5 connections to prescriber.

Conclusion
Physicians who shared patients with many other physicians were more likely to prescribe ARNI, independent of physicians’ specialty. This suggested that collaboration and exchange on the basis of patient-sharing with other physicians influenced their medication prescribing decisions.
Outcome of intracerebral cavernoma treated by Gamma Knife radiosurgery based on a double-blind assessment of treatment indication
Authors: Shen Chiung-Chyi , Sun Ming Hsi , Yang Meng-Yin , You Weir-Chiang , Sheu Meei-Ling , Chen Yen-Ju , Chen Ying Ju , Sheehan Jason , Pan Hung-Chuan 
Published: August 2021

Abstract
Background
The benefit and the risk profile of Gamma Knife radiosurgery (GKRS) for intracerebral cavernoma remains incompletely defined in part due to the natural history of low incidence of bleeding and spontaneous regression of this vascular malformation. In this study, we retrieved cases from a prospectively collected database to assess the outcome of intracerebral cavernoma treated with GKRS using a double blinded review process for treatment.

Methods
From 2003 to 2018, there were 94 cases of cavernoma treated by GKRS in the doubly blinded assessments by two experienced neurological and approved for GKRS treatment. All the patients received GKRS with margin dose of 11–12 (Gray) Gy and afterwards were assessed for neurological outcome, radiologic response, and quality of life.

Results
The median age of the patients was 48 (15–85) years with median follow up of 77 (26–180) months post SRS. The mean target volume was 1.93 ± 3.45 cc. In those who has pre-SRS epilepsy, 7 of 16 (43.7%) achieved seizure freedom (Engel I/II) and 9 of 16 (56.3%) achieved decreased seizures (Engel III) after SRS. Rebleeding occurred in 2 cases (2.1%) at 13 and 52 months post SRS. The radiologic assessment demonstrated 20 (21.3%) cases of decreased cavernoma volume, 69 (73.4%) were stable, and 5 (7.3%) increased size. Eighty-seven of 94 (92.5%) cases at the last follow up achieve improvement in their quality of life, but 7 cases (7.4%) showed a deterioration. In statistical analysis, the effective seizure control class (Engel I/II) was highly correlated with patient harboring a single lesion (p < 0.05) and deep seated location of the cavernoma (p < 0.01). New neurological deficits were highly correlated with decreased mental (p < 0.001) and physical (p < 0.05) components of quality of life testing, KPS (p < 0.001), deep seated location (p < 0.01), and increased nidus volume (p < 0.05). Quality of life deterioration either in physical component (p < 0.01), mental component (p < 0.01), and KPS (p < 0.05) was highly correlated with increased cavernoma volume.

Conclusion
Low margin dose GKRS for intracerebral cavernoma offers reasonable seizure control and improved quality of life while conferring a low risk of treatment complications including adverse radiation effect.
Systematic review of the efficacy of a hybrid operating theatre in the management of severe trauma
Authors: Khoo Chun Yuet , Liew Terence Yi Song , Mathur Sachin 
Published: August 2021

Abstract
Background
Hybrid operating theatres (OT) allow for simultaneous interventional radiology and operative procedures, serving as a one-stop facility for the treatment of severely injured patients. Several countries have adopted the use of the hybrid OT however their clinical impact in improving efficiency and quality of care remains unclear. This study systematically reviews the clinical impact of the hybrid OT for treatment of the severely injured.

Methods
A literature review of the PubMed, Embase and Cochrane databases was performed to identify all published articles in English, from 1st January 2000 to 31st December 2020, reporting on the impact of a hybrid OT for severe trauma. Articles were also reviewed for references of interest.

Results
Five studies reporting the clinical impact of the hybrid OT, in a total of 951 patients, were shortlisted. All were cohort studies that compared patient outcomes in the hybrid OT versus a conventional group. Out of 3 studies that assessed timeliness to intervention, one reported shorter time associated with the hybrid OT, while the other two reported no difference. Mortality outcomes were reported in 4 studies and showed no significant difference associated with treatment in the hybrid OT. Two studies revealed shorter total procedure times associated with the hybrid OT. Two out of 3 studies that evaluated blood transfusion requirements reported decreased transfusion rates in the hybrid OT group. Only 1 study examined complication rates and demonstrated morbidity benefits associated with the hybrid OT.

Conclusion
Establishment of a hybrid OT requires a significant capital investment as well as a highly functioning multi-disciplinary team. The cost–benefit ratio remains unclear. Future studies, preferably in the form of clinical trials, are required to evaluate its usefulness in improving timeliness to definitive haemorrhage control and outcomes in severe trauma.
Double left brachiocephalic vein in an adult patient who underwent cardiac surgery: a case report
Authors: Kobayashi Kimihiro , Uchida Tetsuro , Kuroda Yoshinori , Yamashita Atushi , Ohba Eiichi , Nakai Shingo , Ochiai Tomonori , Sadahiro Mitsuaki 
Published: August 2021

Abstract
Background
A double left brachiocephalic vein is an extremely rare venous anomaly.

Case presentation
Herein, we present the case of a 79-year-old woman with a double left brachiocephalic vein who underwent cardiac surgical procedures. The normal left brachiocephalic vein was patent, and the accessory left brachiocephalic vein passed across the heart and aorta in front of the pericardium and drained into the superior vena cava. She underwent surgical ligation of the accessory left brachiocephalic vein, followed by an aortic valve replacement and coronary artery bypass grafting. Her postoperative recovery was uneventful, without any venous complications from the ligation of the accessory vein. The patient is doing well one year after the surgery.

Conclusions
The presence of double left brachiocephalic veins should be recognized before cardiac surgery in order for us to avoid intraoperative technical issues concerning this venous anomaly and unpredictable intraoperative bleeding due to injury of the accessory left brachiocephalic vein.
Extracellular protein components of amyloid plaques and their roles in Alzheimer’s disease pathology
Authors: Rahman M. Mahafuzur , Lendel Christofer 
Published: August 2021

AbstractAlzheimer’s disease (AD) is pathologically defined by the presence of fibrillar amyloid β (Aβ) peptide in extracellular senile plaques and tau filaments in intracellular neurofibrillary tangles. Extensive research has focused on understanding the assembly mechanisms and neurotoxic effects of Aβ during the last decades but still we only have a brief understanding of the disease associated biological processes. This review highlights the many other constituents that, beside Aβ, are accumulated in the plaques, with the focus on extracellular proteins. All living organisms rely on a delicate network of protein functionality. Deposition of significant amounts of certain proteins in insoluble inclusions will unquestionably lead to disturbances in the network, which may contribute to AD and copathology. This paper provide a comprehensive overview of extracellular proteins that have been shown to interact with Aβ and a discussion of their potential roles in AD pathology. Methods that can expand the knowledge about how the proteins are incorporated in plaques are described. Top-down methods to analyze post-mortem tissue and bottom-up approaches with the potential to provide molecular insights on the organization of plaque-like particles are compared. Finally, a network analysis of Aβ-interacting partners with enriched functional and structural key words is presented.
Taxonomy-based data representation for data mining: an example of the magnitude of risk associated with H. pylori infection
Authors: Polaka Inese , Razuka-Ebela Danute , Park Jin Young , Leja Marcis 
Published: August 2021

Abstract
Background
The amount of available and potentially significant data describing study subjects is ever growing with the introduction and integration of different registries and data banks. The single specific attribute of these data are not always necessary; more often, membership to a specific group (e.g. diet, social ‘bubble’, living area) is enough to build a successful machine learning or data mining model without overfitting it. Therefore, in this article we propose an approach to building taxonomies using clustering to replace detailed data from large heterogenous data sets from different sources, while improving interpretability. We used the GISTAR study data base that holds exhaustive self-assessment questionnaire data to demonstrate this approach in the task of differentiating between H. pylori positive and negative study participants, and assessing their potential risk factors. We have compared the results of taxonomy-based classification to the results of classification using raw data.

Results
Evaluation of our approach was carried out using 6 classification algorithms that induce rule-based or tree-based classifiers. The taxonomy-based classification results show no significant loss in information, with similar and up to 2.5% better classification accuracy. Information held by 10 and more attributes can be replaced by one attribute demonstrating membership to a cluster in a hierarchy at a specific cut. The clusters created this way can be easily interpreted by researchers (doctors, epidemiologists) and describe the co-occurring features in the group, which is significant for the specific task.

Conclusions
While there are always features and measurements that must be used in data analysis as they are, the use of taxonomies for the description of study subjects in parallel allows using membership to specific naturally occurring groups and their impact on an outcome. This can decrease the risk of overfitting (picking attributes and values specific to the training set without explaining the underlying conditions), improve the accuracy of the models, and improve privacy protection of study participants by decreasing the amount of specific information used to identify the individual.