Miracle-dz/UniFAR-FTUs huggingface dataset:
THE RELATION OF LEUKOSIS TO SARCOMA OF CHICKENS

A transmissible strain of sarcoma (Strain 13) is described that took its origin in a chicken inoculated with leukosis of Strain 1. The virus of Strain 13 produces sarcoma in the breast muscle injected with it and after intravenous inoculation it produces diffuse sarcomatosis of the spleen, bone marrow, and several other organs. The available evidence suggests that Strain 13 is caused by a single virus with ability to produce diffuse endothelial growth in the blood-forming organs associated with extensive hematomata, and erythroblastic proliferation. The strain can be readily transmitted by material free from live cells and preserved by drying. As small amounts of blood as 0.00001 cc. from chickens with sarcomatosis of the internal organs transmit Strain 13 by the intravenous route. By implantation sarcoma of Strain 13 can be transferred to chickens that are resistant to repeated inoculations with leukotic viruses.
BIOLITMAP: a web-based geolocated, temporal and thematic visualization of the evolution of bioinformatics publications

Abstract Motivation The fast growth of bioinformatics adds a significant difficulty to assess the contribution, geographical and thematic distribution of the research publications. Results To help researchers, grant agencies and general public to assess the progress in bioinformatics, we have developed BIOLITMAP, a web-based geolocation system that allows an easy and sensible exploration of the publications by institution, year and topic. Availability and implementation BIOLITMAP is available at http://socialanalytics.bsc. es/biolitmap and the sources have been deposited at https://github.com/inab/BIOLITMAP. Supplementary information Supplementary data are available at Bioinformatics online.
Effectiveness of the Devolved Primary Health Care Gatekeeper System in Machakos County, Kenya

The low health outcomes and inequities problems in developing countries are due to ineffective gate keeping at the Primary Health Care (PHC) level, non-adherence to policy and dysfunctional health infrastructure. This study was conducted at 100 PHC centres sampled using Taro Yamane formula, in Machakos County, Kenya, from March to May 2015. It involved 8 gender-based focus group discussions (FGDs) with patients and their caretakers. Qualitative and quantitative data were collected from emancipated children and adults aged 15-65 years excluding the disabled due to data integrity issues. The Statistical Package for Social Science (SPSS) version 20.0 and Atlas.ti 7 software were used for data analysis. Correlation was done using the Spearman rho test and significance was set at <0.05. A questionnaire return rate of 83% was achieved of whom 84.3% were nurses (p<0.001) nurses and 15.7% were diploma holders in clinical medicine (clinical officers). The health workers were young (P<0.001) and married (p<0.001). A proportional relationship (rho=0.383, p< .001) existed between the number of out-patients received and cases referred to hospitals. Most gatekeepers were ignorant (p=0.04) about the Policy on the patients’ referral yet they did not officially refer patients (80.7%). Most (63.5%) of the hospitals receiving self-referrals did not ask for referral letters. Policy and referral letters were found to be necessary (p=0.004). The gatekeepers’ non-adherence to policy, lack of laboratory services and shortages of drugs contributed to self-referral by patients, creating a burden on the resources for healthcare, resulting in inefficiency at the PHC level. This study recommends a review of the gatekeeping system at the PHC level, capacity building, quality assurance, redefinition and strengthening of the office of the gatekeepers, regularization of supplies and reinforcement of the patient referral policy, staff motivation and best practices in customer care.
When to use next generation sequencing or diagnostic PCR in diet analyses

Next‐generation sequencing (NGS) is increasingly used for diet analyses; however, it may not always describe diet samples well. A reason for this is that diet samples contain mixtures of food DNA in different amounts as well as consumer DNA which can reduce the food DNA characterized. Because of this, detections will depend on the relative amount and identity of each type of DNA. For such samples, diagnostic PCR will most likely give more reliable results, as detection probability is only marginally dependent on other copresent DNA. We investigated the reliability of each method to test (a) whether predatory beetle regurgitates, supposed to be low in consumer DNA, allow to retrieve prey sequences using general barcoding primers that co‐amplify the consumer DNA, and (b) to assess the sequencing depth or replication needed for NGS and diagnostic PCR to give stable results. When consumer DNA is co‐amplified, NGS is better suited to discover the range of possible prey, than for comparing co‐occurrences of diet species between samples, as retested samples were repeatedly different in prey detections with this approach. This shows that samples were incompletely described, as prey detected by diagnostic PCR frequently were missed by NGS. As the sequencing depth needed to reliably describe the diet in such samples becomes very high, the cost‐efficiency and reliability of diagnostic PCR make diagnostic PCR better suited for testing large sample‐sets. Especially if the targeted prey taxa are thought to be of ecological importance, as diagnostic PCR gave more nested and consistent results in repeated testing of the same sample.
Dexmedetomidine Use in a Tertiary Care NICU: A Descriptive Study

Background: Continuous infusions of dexmedetomidine are increasingly used for sedation in critically ill pediatric patients. Emerging data suggest potential benefits when used for sedation in neonates, including reduced sedative requirements and earlier enteral feeds. Objective: To describe the use, adverse effects, and signs of withdrawal in a cohort of neonates receiving dexmedetomidine, the majority of whom were receiving concomitant opioids. Methods: This was a retrospective, descriptive review of 38 neonates receiving dexmedetomidine in a medical surgical neonatal intensive care unit, including data on duration of use, dose, adverse effects, weaning, and signs of withdrawal. Results: Dexmedetomidine was used for a median of 183 hours, at a median maximum dose of 0.5 µg/kg/h. Premature infants were started on dexmedetomidine at a later chronological age than term infants (41 vs 9 days, P = 0.004). Of 18 patients receiving an opioid infusion at the time of dexmedetomidine initiation, 67% had a dose reduction in opioids by 24 hours. The majority (89%) of neonates had at least 1 potentially related adverse effect during the dexmedetomidine infusion, though no discontinuations were needed as a result. In all, 80% of patients had their dexmedetomidine gradually weaned off, and 71% had at least 1 sign of withdrawal. Conclusions and Relevance: In this cohort, dexmedetomidine was often used in a postsurgical setting, with concomitant opioids, over prolonged periods. These factors appear to affect and likely confound the rates of adverse effects and withdrawal signs from dexmedetomidine. Clinicians considering the use of dexmedetomidine in a similar population can draw guidance from our data.
Different Isoforms of the Neuronal Guidance Molecule Slit2 Directly Cause Chemoattraction or Chemorepulsion of Human Neutrophils

The movement of neutrophils between blood and tissues appears to be regulated by chemoattractants and chemorepellents. Compared with neutrophil chemoattractants, relatively little is known about neutrophil chemorepellents. Slit proteins are endogenously cleaved into a variety of N- and C-terminal fragments, and these fragments are neuronal chemorepellents and inhibit chemoattraction of many cell types, including neutrophils. In this report, we show that the ∼140-kDa N-terminal Slit2 fragment (Slit2-N) is a chemoattractant and the ∼110-kDa N-terminal Slit2 fragment (Slit2-S) is a chemorepellent for human neutrophils. The effects of both Slit2 fragments were blocked by Abs to the Slit2 receptor Roundabout homolog 1 or the Slit2 coreceptor Syndecan-4. Slit2-N did not appear to activate Ras but increased phosphatidylinositol 3,4,5-triphosphate levels. Slit2-N–induced chemoattraction was unaffected by Ras inhibitors, reversed by PI3K inhibitors, and blocked by Cdc42 and Rac inhibitors. In contrast, Slit2-S activated Ras but did not increase phosphatidylinositol 3,4,5-triphosphate levels. Slit2-S–induced chemorepulsion was blocked by Ras and Rac inhibitors, not affected by PI3K inhibitors, and reversed by Cdc42 inhibitors. Slit2-N, but not Slit2-S, increased neutrophil adhesion, myosin L chain 2 phosphorylation, and polarized actin formation and single pseudopods at the leading edge of cells. Slit2-S induced multiple pseudopods. These data suggest that Slit2 isoforms use similar receptors but different intracellular signaling pathways and have different effects on the cytoskeleton and pseudopods to induce neutrophil chemoattraction or chemorepulsion.
A String Kernel based Information Retrieval Approach for Tweet-validation through News

Micro-blogging websites like Twitter are very popular among internet users, over 100 million tweets are posted every day. The websites are active in e cient dissemination of information pertinent to any emergency like ood and earthquake. Recent research proved that these platforms can e ectively be used for monitoring, evaluations and coordinating relief operations in such situations. One of the very critical issue of such applications is to identifying the validity of these posts automatically during the emergency situation as factual information or rumors. The idea is to verify the tweet from some other authentic news source. Forum for Information Retrieval Evaluation (FIRE 2018) edition included a shared task for Information Retrieval from Microblogs during Disasters (IRMiDis). The subtask 1, is identifying the tweets from their content as fact or fact-checkable tweets. The main idea of this task is to identify the validity of the tweets so that the rumors or baseless situational tweets can be ltered from the context of monitoring and response activity of such challenging emergency situations. The paper proposes a string kernel based information retrieval approach for tweet-validation through NEWS. Our approach is based on two-steps information retrieval. In rst step, we consider a given tweet as a query and nd a best matching headline using Aho-Corasick algorithm with a score greater than . In the next step, we matched the content of the news with the tweet using cosine similarity, if this score is also greater than , it means that we have a supporting news item for the given tweet. We learn the values of α=0.11 and β=0.25 through experimentation. Our proposed approach performed second best in the competition with overall NDGC 0.667.
Arterial stiffness in adult patients after coarctation of aorta repair and with bicuspid aortic valve

Abstract Objectives: The coarctation of aorta is commonly related to bicuspid aortic valve. The aim of the study was to assess arterial stiffness in adults after aortic coarctation repair and to evaluate an impact of bicuspid aortic valve concomitance on arterial stiffness results. Methods: Fifty-eight patients after coarctation of aorta repair, 36 male, median age of 27.46 ± 10.57, were compared to 30 with bicuspid aortic valve and to 30 healthy, sex, age and BMI matched volunteers. Physical examination, laboratory analysis and non-invasive assessment of arterial stiffness were performed. Results: CoA patients and BAV patients have higher central arterial stiffness parameters in comparison to healthy controls: AP (7.86 ± 6.56 vs 7.68 ± 5.96 vs 1.41 ± 3.82 mmHg, p < 0.001, p = 0.011, respectively) and AIx (18.81 ± 14.94 vs 18.06 ± 13.38 vs 4.41 ± 10.82%, p < 0.001, p = 0.006, respectively). There were no differences of PWV between CoA patients, BAV patients and healthy controls (6.07 ± 1.20 vs 5.95 ± 1.20 vs 5.67 ± 0.73 m/s, p = 0.099, p = 0.278, respectively). In CoA group, there was correlation of PWV with age (r = 0.55 p < 0.001), BMI (r = 0.29, p = 0.025), fibrinogen (r = 0.31, p = 0.039), glucose (r = 0.58, p < 0.001), ascending aorta diameter (r = 0.29, p = 0.026) and age at operation (r = 0.27, p = 0.041). Among group of BAV, there was a correlation of PWV with age (r = 0.58, p < 0.001), central AP with total cholesterol (r = 0.38, p = 0.036) and fibrinogen (r = 0.41, p = 0.024). Conclusions: The increased arterial stiffness occurs in both groups: patients after aortic coarctation repair and patients with bicuspid aortic valve. Concomitance of coarctation of the aorta and bicuspid aortic valve has no influence on arterial stiffness augmentation.
Military use of tranexamic acid in combat trauma: Does it matter?

BACKGROUND Tranexamic acid (TXA) has been previously reported to have a mortality benefit in civilian and combat-related trauma, and was thus added to the Joint Theater Trauma System Damage Control Resuscitation Clinical Practice Guideline. As part of ongoing system-wide performance improvement, the use of TXA has been closely monitored. The goal was to evaluate the efficacy and safety of TXA use in military casualties and provide additional guidance for continued use. METHODS A total of 3,773 casualties were included in this retrospective, observational study of data gathered from a trauma registry. The total sample, along with three subsamples for massive transfusion patients (n = 784), propensity-matched sample (n = 1,030), and US/North Atlantic Treaty Organization (NATO) military (n = 1,262), was assessed for administration of TXA and time from injury to administration of TXA. Outcomes included mortality and occurrence of pulmonary embolism and deep vein thrombosis. Multivariable proportional hazards regression models with robust standard error estimates were used to estimate hazard ratios (HR) for assessment of outcomes while controlling for covariates. RESULTS Results of univariate and multivariate analyses of the total sample (HR, 0.97; 95% confidence interval [CI], 0.62–1.53; p = 0.86), massive transfusion sample (HR, 0.84; 95% CI, 0.46–1.56; p = 0.51), propensity-matched sample (HR, 0.68; 95% CI, 0.27–1.73; p = 0.34), and US/NATO military sample (HR, 0.76; 95% CI, 0.30–1.92; p = 0.48) indicate no statistically significant association between TXA use and mortality. Use of TXA was associated with increased risk of pulmonary embolism in the total sample (HR, 2.82; 95% CI, 2.08–3.81; p < 0.001), massive transfusion sample (HR, 3.64; 95% CI, 1.96–6.78; p = 0.003), US/NATO military sample (HR, 2.55; 95% CI, 1.73–3.69; p = 0.002), but not the propensity-matched sample (HR, 3.36; 95% CI, 0.80–14.10; p = 0.10). TXA was also associated with increased risk of deep vein thrombosis in the total sample (HR, 2.00; 95% CI, 1.21–3.30; p = 0.02) and US/NATO military sample (HR, 2.18; 95% CI, 1.20–3.96; p = 0.02). CONCLUSION In the largest study on TXA use in a combat trauma population, TXA was not significantly associated with mortality, due to lack of statistical power. However, our HR estimates for mortality among patients who received TXA are consistent with previous findings from the CRASH-2 trial. At the same time, continued scrutiny and surveillance of TXA use in military trauma, specifically for prevention of thromboembolic events, is warranted. Level of Evidence Therapeutic, level IV.
The normal range and determinants of the intrinsic heart rate in man.

Normal standards for the intrinsic heart rate (IHR) were measured in 432 healthy adult subjects aged 16 to 70 years. At rest, with normal body temperature, the IHR was highly reproducible. In different subjects, age was the only important determinant. Differences in IHR between individuals may correspond to differences in functional capacity of the myocardium, whether determined genetically, by age, or by disease.
Potential link between Fusobacterium enrichment and DNA methylation accumulation in the inflammatory colonic mucosa in ulcerative colitis

BACKGROUND AND AIM Fusobacterium enrichment has been associated with colorectal cancer development. Ulcerative colitis (UC) associated tumorigenesis is characterized as high degree of methylation accumulation through continuous colonic inflammation. The aim of this study was to investigate a potential link between Fusobacterium enrichment and DNA methylation accumulation in the inflammatory colonic mucosa in UC. METHODS In the candidate analysis, inflamed colonic mucosa from 86 UC patients were characterized the methylation status of colorectal a panel of cancer related 24 genes. In the genome-wide analysis, an Infinium HumanMethylation450 BeadChip array was utilized to characterize the methylation status of >450,000 CpG sites for fourteen UC patients. Results were correlated with Fusobacterium status. RESULTS UC with Fusobacterium enrichment (FB-high) was characterized as high degree of type C (for cancer-specific) methylation compared to other (FB-low/neg) samples (P<0.01). Genes hypermethylated in FB-high samples included well-known type C genes in colorectal cancer, such as MINT2 and 31, P16 and NEUROG1. Multivariate analysis demonstrated that the FB high status held an increased likelihood for methylation high as an independent factor (odds ratio: 16.18, 95% confidence interval: 1.94-135.2, P=0.01). Genome-wide methylation analysis demonstrated a unique methylome signature of FB-high cases irrespective of promoter, outside promoter, CpG and non-CpG sites. Group of promoter CpG sites that were exclusively hypermethylated in FB-high cases significantly codified the genes related to the catalytic activity (P=0.039). CONCLUSION Our findings suggest that Fusobacterium accelerates DNA methylation in specific groups of genes in the inflammatory colonic mucosa in UC.
Medial elbow anatomy: A paradigm shift for UCL injury prevention and management

To improve the management outcomes and diagnostic accuracy of the ulnar collateral ligament (UCL) injury, the anatomy of the medial side of the elbow joint is necessary to be understood in terms of the periarticular surroundings rather than the specific ligaments. The aim of this study was to anatomically clarify the medial side of the elbow joint in terms of the tendinous structures and joint capsule. We conducted a descriptive anatomical study of 23 embalmed cadaveric elbows. We macroscopically analyzed the relationship between the flexor pronator muscles (FPMs) and the joint capsule in 10 elbows, histologically analyzed in 6 elbows, and observed the bone morphology through micro computed tomography in 7 elbows. The two tendinous septa (TS) were found: between the pronator teres (PT) and flexor digitorum superficial (FDS) muscles, and between the FDS and flexor carpi ulnaris (FCU) muscles. These two TS are connected to the medial part of the brachialis tendon, deep aponeurosis of the FDS, and FCU to form the tendinous complex, which linked the humeroulnar joint and could not be histologically separated from each other. Moreover, the capsule of the humeroulnar joint under the tendinous complex had attachment on the ST of 7 mm width. The two TS, the brachialis tendon, the deep FDS and FCU aponeuroses, and the joint capsule linked the humeroulnar joint. These anatomical findings could lead to a paradigm shift in the prevention, diagnosis, and treatment of UCL injuries in baseball players. Clin. Anat. 32:379–389, 2019. © 2018 The Authors. Clinical Anatomy published by Wiley Periodicals, Inc. on behalf of American Association of Clinical Anatomists.
Joint space narrowing, cartilage and physical function: are we deceived by measurements and distributions?

Irreversible physical function loss—that part of physical function loss that remains in the absence of clinically perceptible disease activity—was elegantly conceptualised by Aletaha et al 1 a few years ago. They introduced the idea of the irreversible health assessment questionnaire (HAQ) score, which is the residual HAQ score if a patient is in clinical remission. While one may argue the construct validity of an irreversible HAQ score (eg, the absence of clinical disease activity does not necessarily imply the absence of joint inflammation), the model is valuable because it allows the investigator to disentangle the contribution of signs and symptoms and that of structural damage on physical function. From many studies performed during the past 10 years we have learnt that structural joint damage independently of disease activity contributes to explaining physical function (eg, Welsing et al ). 2 Therefore, in the absence of disease activity, it is structural joint damage that explains irreversible physical function loss. Aletaha et al 1 have taken up his hypothesis as a starting point, and have tried to unravel the relationship between the two components of radiographic damage—erosions and joint space narrowing (JSN)—and irreversible physical function loss. The analysis they have done, which is presented in this issue of the journal, is in all aspects provocative and challenging, and we truly commend the authors for taking up this exercise (see page 733). Strong elements of their study are the access to databases of large clinical trials with inherently high-quality data and completeness, as well as a hypothesis-driven approach. It is a broadly endorsed idea among clinicians that JSN matters more than erosions. So, the main conclusion of the analysis by Aletaha et al ,1 namely that JSN more than erosions impacts irreversible physical function loss, will be easily accepted by the clinical readership. …
Systemic Acquired Resistance.

Systemic acquired resistance (SAR) refers to a distinct signal transduction pathway that plays an important role in the ability of plants to defend themselves against pathogens. After the formation of a necrotic lesion, either as a part of the hypersensitive response (HR) or as a symptom of disease, the SAR pathway is activated. SAR activation results in the development of a broad-spectrum, systemic resistance (Hunt and Ryals, 1996; Neuenschwander et al., 1996). Although SAR is interesting as a paradigm for signal transduction, it may have practical value as well. An understanding of the biochemical changes leading to the resistance state could enable the development of either genetically engineered plants with enhanced disease resistance or novel mode-of-action plant protection chemicals that act by stimulating the plant's inherent disease resistance mechanisms. SAR can be distinguished from other disease resistance responses by both the spectrum of pathogen protection and the associated changes in gene expression. In tobacco, SAR activation results in a significant reduction of disease symptoms caused by the fungi Phytophthora parasifica, Cercospora nicotianae, and Peronospora tabacina, the viruses tobacco mosaic virus (TMV) and tobacco necrosis virus (TNV), and the bacteria Pseudomonas syringae pv tabaci and Erwinia carotovora (Vernooij et al., 1995). However, the protection is not effective against all pathogens. For example, there is no significant protection against either Botrytis cinerea or Alternaria alternata. Thus, SAR provides resistance against seven of nine tobacco pathogens, establishing a distinctive fingerprint of protection. Associated with SAR is the expression of a set of genes called SAR genes (Ward et al., 1991). However, not all defenserelated genes are expressed during SAR, and the particular spectrum of gene expression therefore distinguishes the SAR response from other resistance responses in plants. Tobacco is perhaps the best characterized model for SAR, but other plants respond similarly. For example, in Arabidopsis, SAR is effective against F! parasitica, F! syringae pv tomato DC3000, and turnip crinkle virus, and the associated SAR genes are a subset of those expressed in tobacco (Uknes et al., 1992).