Miracle-dz/UniFAR-FTUs huggingface dataset:
FTA-Sodium hydroxide-based polymerase chain reaction (PCR): An efficient and cheaper option for Theileria parva detection in dairy cattle in Mbarara, Uganda

East Coast fever is caused by Theileria parva, and poses serious concerns for dairy farmers owing to massive economic losses. In the current study, we compared three methods (DNA extraction kits, FTA-NaOH and FTA-TENT) of DNA extraction to identify the most economical and reliable method. A survey for T. parva prevalence was conducted in dairy cattle in Mbarara, Uganda. Cytochrome C oxidase subunit I (COI) and T. parva-p104 genes were amplified to compare the methods. FTA-NaOH-based polymerase chain reaction (PCR) yielded the best detection rate for both COI gene and p104 gene. Prevalence of T. parva was 45.0% and 83.3% at animal and farm-level, respectively. FTA-NaOH based-PCR is simple, highly sensitive and cost-effective tool for T. parva diagnosis in resource constrained settings.
Mechanical characterisation of an organic phantom candidate for breast tissue

The aim of this study is to analyse the mechanical properties of agarose, which can be used as a mechanical phantom for breast tissues. In general, tissue mimicking materials may be used to achieve a better understanding of the structure and properties of tissues and organs; this work shares these objectives. The phantom can be used as a tissue surrogate with realistic mechanical behaviour for biomechanical applications. To validate agarose as a suitable mechanical phantom for breast tissues, indentation tests were performed in homogeneous, rectangular agarose blocks. Blocks with different agarose concentrations were moulded and tested. An estimation of the material stiffness was then compared with experimental data on different breast tissues’ types found in literature. The phantom stiffness increased consistently with agarose concentration and stress. The results show that agarose-based mechanical phantoms of stiffer tissues require higher agarose concentrations (0.5% and 0.6%). In contrast, normal tissues can be mimicked with 0.3% and 0.4% of agarose. In addition, it was observed that preconditioning affects the mechanical properties of the gel, as it had already been shown in literature for breast tissues.
In-depth phylogenetic analysis of the hemagglutinin gene of influenza A(H3N2) viruses circulating during the 2016-2017 season revealed egg-adaptive mutations of vaccine strains

ABSTRACT Objectives: The authors conducted an in-depth phylogenetic analysis of the hemagglutinin (HA) gene of A(H3N2) identified during the 2016–2017 season to compare the circulating strains with both the egg-derived and cell-derived 2016–2017 candidate vaccine virus (CVV). Methods: 162 HA1 sequences of H3N2 viruses identified during the 2016–2017 season were phylogenetically analyzed and compared with egg-/cell-derived CVV. The predicted vaccine efficacy (pVE) of egg-/cell-derived CVV against field strains was quantified by Pepitope model. Results: All H3N2 belonged to 3C.2a genetic clade, most (80.2%) to 3C.2a1 sub-clade. Several H3N2 variants circulated in the 2016–2017 season. HA sequences of field H3N2 strains displayed greater identity with cell-derived CVV than with egg-derived CVV. The amino acid substitutions in positions 160 and 194 identified in egg-derived CVV affected the pVE, which was lower for egg-derived CVV than for cell-derived CVV. Conclusions: The results suggested that reduced vaccine effectiveness observed in 2016–2017 season was probably due to changes in the HA of vaccine strains acquired upon adaptation in eggs, which are the basis of most manufacturing systems currently used globally. Egg-free vaccine manufacturing systems would be advisable to improve the effectiveness of influenza vaccines.
Coagulation Factor Xa (Recombinant), Inactivated-Zhzo (Andexanet Alfa) Hemostatic Outcomes and Thrombotic Event Incidence at an Academic Medical Center

Andexanet alfa is approved for the reversal of factor Xa inhibitors in patients with major bleeding events. We aimed to review the incidence of effective hemostasis with andexanet alfa in a real-world environment. This retrospective cohort included patients hospitalized for a major bleed that resulted in andexanet alfa administration. The primary outcome was effective hemostasis at 12 hours after andexanet alfa treatment. Thromboembolic events and mortality within 30 days were also assessed. Over a 14-month period, 13 patients received andexanet alfa with a mean age of 69 ± 10 years, 54% male, 69% exposed to apixaban (31% rivaroxaban), and had intracranial (46%) and nonintracranial (54%) bleeding sites. Effective hemostasis was observed in 10 (77%) patients. Four (31%) patients experienced 5 thromboembolic events with a median time to event of 6.5 days (range: 0.5-29). Four thrombotic events occurred during the period in which anticoagulation (prophylaxis or therapeutic) was not restarted. Mortality rate was 15%. Andexanet alfa was effective in obtaining hemostasis in a majority of patients. However, the incidence of thromboembolic events was high and may be attributed to a delay in restarting anticoagulation.
Pilot study of docetaxel combined with lobaplatin or gemcitabine for recurrent and metastatic breast cancer

Abstract Background: This study evaluated the efficacy and safety of docetaxel combined with lobaplatin, relative to docetaxel combined with gemcitabine, for treating patients with recurrent metastatic breast cancer (rMBC). Methods: Patients with rMBC received ≥2 cycles (21 days each) of either docetaxel and lobaplatin (DL; n = 21), or docetaxel and gemcitabine (DG; n = 22). On day 1 of each cycle, all patients were given 75 mg/m2 intravenous docetaxel. Patients in DL and DG were also given, respectively, 35 mg/m2 intravenous lobaplatin (day 2) or 1000 mg/m2 intravenous gemcitabine (days 1, 8). Results: Five (11.6%) and 16 (37.2%) patients achieved complete remission and partial response, respectively; rates of response and disease control were 48.8%. The response rates of the groups were comparable (47.6%, 50.0%). The median survival times after relapse and metastasis of the DL group (18 months) were significantly less than that of the DG group (25 months). Median progression-free survivals after relapse and metastasis were similar (12 cf. 14 months). The main toxic side reaction was grade 2, with no treatment-related deaths. Rates of the following were comparable between DG and DL: grade 3 or 4 white blood cells (23.8%, 31.8%) and digestive tract toxicity (4.8%, 4.5%); neutropenia (28.6%, 22.7%); anemia (4.8%, nil); and thrombocytopenia (19.0%, 13.6%). Other toxicities included hepatic toxicity, myalgia, infection, and fatigue. Conclusions: Both the DL and DG regimens were associated with encouraging benefits, while treatment-related toxicity was manageable. Therefore, these regimens are effective options for treatment of rMBC. Trial registration: This clinical trial study was approved by the Ethics Committee of Guizhou Cancer Hospital, and has been registered in the China Clinical Trial Center (December 8, 2014, No. ChiCTR-IPR-14005633).
Verification a model of predicting vaginal birth after cesarean delivery in Chinese pregnant women

Abstract The objective of our research was to confirm the prediction role of Grobman model for vaginal birth after cesarean (VBAC) in Chinese pregnant women. In this research, 535 pregnant who had once cesarean delivery and the least once subsequent try to a vaginal labor in Jiaxing of China were involved. The Grobman background factors and five new factors were included. Overall, in total of 456 women had successful VBAC, the success percent was 85.2%. The new background variable “maternal height” was considered as an additional predictor for VBAC. The Grobman model's area under the curve (AUC) was 0.811 (95% CI = 0.751–0.870) and the AUC of this modified model combined 2 new factors was 0.834 (95% CI = 0.781–0.886). Nevertheless, there has no markedly difference between these 2 models of the AUC. In conclusion, the Grobman model was suitable for Chinese pregnant. However, further improvements were needed to make a new predictive model of VBAC success rate for Chinese pregnant women through analyzing the clinical data of vaginal trial delivery after cesarean section.
Impact of sex on diabetic nephropathy and the renal transcriptome in UNx db/db C57BLKS mice

Diabetic nephropathy (DN) is associated with albuminuria and loss of kidney function and is the leading cause of end‐stage renal disease. Despite evidence of sex‐associated differences in the progression of DN in human patients, male mice are predominantly being used in preclinical DN research and drug development. Here, we compared renal changes in male and female uninephrectomized (UNx) db/db C57BLKS mice using immunohistochemistry and RNA sequencing. Male and female UNx db/db mice showed similar progression of type 2 diabetes, as assessed by obesity, hyperglycemia, and HbA1c. Progression of DN was also similar between sexes as assessed by kidney and glomerular hypertrophy as well as urine albumin‐to‐creatinine ratio being increased in UNx db/db compared with control mice. In contrast, kidney collagen III and glomerular collagen IV were increased only in female UNx db/db as compared with respective control mice but showed a similar tendency in male UNx db/db mice. Comparison of renal cortex transcriptomes by RNA sequencing revealed 66 genes differentially expressed (p < .01) in male versus female UNx db/db mice, of which 9 genes were located on the sex chromosomes. In conclusion, male and female UNx db/db mice developed similar hallmarks of DN pathology, suggesting no or weak sex differences in the functional and structural changes during DN progression.
Comparative Effectiveness of Two Collagen-containing Dressings: Oxidized Regenerated Cellulose (ORC)/Collagen/Silver-ORC Dressing Versus Ovine Collagen Extracellular Matrix.

INTRODUCTION Chronic wounds are characterized by impaired tissue physiology that stalls healing. The prevalence of wound chronicity presents challenges in wound management and health care cost-containment. OBJECTIVE This comparative effectiveness study evaluates the value proposition of 2 collagen-containing wound dressings - oxidized regenerated cellulose (ORC)/collagen/silver-ORC dressing and ovine collagen extracellular matrix (ECM) - in matched cohorts of patients undergoing treatment for diabetic foot ulcers (DFUs). MATERIALS AND METHODS Data extracted from the US Wound Registry identified DFUs treated with either dressing and included wounds with complete data records (n = 3230). Thirty-seven variables were considered in propensity score matching to develop a case-matched cohort of 844 DFUs (n = 422 DFUs/group). RESULTS The ORC/collagen/silver-ORC dressing group yielded a significantly higher percentage of DFUs that healed or improved (82% vs. 74.6%; P = .0096). The ovine collagen ECM dressing group yielded a significantly higher percentage of DFUs that worsened (15.2% vs. 23.9%; P = .0013). The ORC/collagen/silver-ORC dressing group demonstrated a higher percentage of DFUs that attained 75% to 100% granulation at zero depth at 4, 8, 12, and 16 weeks. Median time to 75% to 100% granulation was 42 days for the ORC/collagen/silver-ORC dressing group versus 60 days for the ovine collagen ECM dressing group (P = .0109). CONCLUSIONS According to this comparative effectiveness study using real world data, ORC/collagen/silver-ORC dressing appears to afford improved healing and reduced time to granulation relative to ovine collagen ECM dressing.
Plasmodium falciparum Gametocyte Density and Infectivity in Peripheral Blood and Skin Tissue of Naturally Infected Parasite Carriers in Burkina Faso

Abstract Background Plasmodium falciparum transmission depends on mature gametocytes that can be ingested by mosquitoes taking a blood meal on human skin. Although gametocyte skin sequestration has long been hypothesized as important contributor to efficient malaria transmission, this has never been formally tested. Methods In naturally infected gametocyte carriers from Burkina Faso, we assessed infectivity to mosquitoes by direct skin feeding and membrane feeding. We directly quantified male and female gametocytes and asexual parasites in finger-prick and venous blood samples, skin biopsy samples, and in of mosquitoes that fed on venous blood or directly on skin. Gametocytes were visualized in skin tissue with confocal microscopy. Results Although more mosquitoes became infected when feeding directly on skin then when feeding on venous blood (odds ratio, 2.01; 95% confidence interval, 1.21–3.33; P = .007), concentrations of gametocytes were not higher in the subdermal skin vasculature than in other blood compartments; only sparse gametocytes were observed in skin tissue. Discussion Our data strongly suggest that there is no significant skin sequestration of P. falciparum gametocytes. Gametocyte densities in peripheral blood are thus informative for predicting onward transmission potential to mosquitoes and can be used to target and monitor malaria elimination initiatives.
Rôle du système immunitaire dans les maladies à prions

Les encephalopathies spongiformes subaigues transmissibles (ESST) se presentent comme des maladies neurodegeneratives du systeme nerveux central, sans syndrome inflammatoire associe, avec un double determinisme genetique et infectieux. Pourtant, les observations les plus recentes mettent l'accent sur l'importance du systeme immunitaire dans la physiopathologie des ESST, tant au niveau peripherique, dans la replication initiale de l'agent, qu'au niveau central dans l'apparition des lesions cerebrales degeneratives associees a une accumulation de l'isoforme pathologique (PrP Sc ) d'une proteine ubiquitaire de l'hote (PrP C ). Ces resultats, qui s'opposent au role direct de la PrP Sc dans la formation des lesions cerebrales, pourraient conduire a reconsiderer les possibilites de transmission par transfusion sanguine.
Seizure Detection Algorithms in Critically Ill Children: A Comparative Evaluation.

OBJECTIVES To evaluate the performance of commercially available seizure detection algorithms in critically ill children. DESIGN Diagnostic accuracy comparison between commercially available seizure detection algorithms referenced to electroencephalography experts using quantitative electroencephalography trends. SETTING Multispecialty quaternary children's hospital in Canada. SUBJECTS Critically ill children undergoing electroencephalography monitoring. INTERVENTIONS Continuous raw electroencephalography recordings (n = 19) were analyzed by a neurophysiologist to identify seizures. Those recordings were then converted to quantitative electroencephalography displays (amplitude-integrated electroencephalography and color density spectral array) and evaluated by six independent electroencephalography experts to determine the sensitivity and specificity of the amplitude-integrated electroencephalography and color density spectral array displays for seizure identification in comparison to expert interpretation of raw electroencephalography data. Those evaluations were then compared with four commercial seizure detection algorithms: ICTA-S (Stellate Harmonie Version 7; Natus Medical, San Carlos, CA), NB (Stellate Harmonie Version 7; Natus Medical), Persyst 11 (Persyst Development, Prescott, AZ), and Persyst 13 (Persyst Development) to determine sensitivity and specificity in comparison to amplitude-integrated electroencephalography and color density spectral array. MEASUREMENTS AND MAIN RESULTS Of the 379 seizures identified on raw electroencephalography, ICTA-S detected 36.9%, NB detected 92.3%, Persyst 11 detected 75.9%, and Persyst 13 detected 74.4%, whereas electroencephalography experts identified 76.5% of seizures using color density spectral array and 73.7% using amplitude-integrated electroencephalography. Daily false-positive rates averaged across all recordings were 4.7 with ICTA-S, 126.3 with NB, 5.1 with Persyst 11, 15.5 with Persyst 13, 1.7 with color density spectral array, and 1.5 with amplitude-integrated electroencephalography. Both Persyst 11 and Persyst 13 had sensitivity comparable to that of electroencephalography experts using amplitude-integrated electroencephalography and color density spectral array. Although Persyst 13 displayed the highest sensitivity for seizure count and seizure burden detected, Persyst 11 exhibited the best trade-off between sensitivity and false-positive rate among all seizure detection algorithms. CONCLUSIONS Some commercially available seizure detection algorithms demonstrate performance for seizure detection that is comparable to that of electroencephalography experts using quantitative electroencephalography displays. These algorithms may have utility as early warning systems that prompt review of quantitative electroencephalography or raw electroencephalography tracings, potentially leading to more timely seizure identification in critically ill patients.
Neutralization of transforming growth factor (TGF)-β1 activity reduced fibrosis and enhanced regeneration of glycerol-injured rat muscle

Recently, we have shown that glycerol induces early fibrosis in rat muscles which persists up to two weeks after injury. The current study aims to determine the possible factor associated with fibrosis of rat muscle following glycerol injury. Eight-week-old male Wistar rats received either glycerol only (as a control) or a co-treatment of neutralizing antibody to transforming growth factor (TGF)-β1 (5 and 12.5 µg). Both antibody doses significantly decreased fibrosis and improved muscle regeneration suggesting that anti-TGF-β1 antibody has both anti-fibrotic and myogenic effects. In conclusion, fibrosis developed in glycerol-injured rat muscles, might be mediated, in part, by the upregulation of TGF-β1 expression. Targeting TGF-β1 could be a promising approach for inhibiting fibrosis and enhancing muscle regeneration.
Proteinase K resistant cores of prions and amyloids

ABSTRACT Amyloids and their infectious subset, prions, represent fibrillary aggregates with regular structure. They are formed by proteins that are soluble in their normal state. In amyloid form, all or part of the polypeptide sequence of the protein is resistant to treatment with proteinase K (PK). Amyloids can have structural variants, which can be distinguished by the patterns of their digestion by PK. In this review, we describe and compare studies of the resistant cores of various amyloids from different organisms. These data provide insight into the fine structure of amyloids and their variants as well as raise interesting questions, such as those concerning the differences between amyloids obtained ex vivo and in vitro, as well as the manner in which folding of one region of the amyloid can affect other regions.
Circulatory Loop Design and Components Introduce Artifacts Impacting In-Vitro Evaluation of Ventricular Assist Device Thrombogenicity: A Call for Caution.

Mechanical circulatory support (MCS) devices continue to be hampered by thrombotic adverse events, a consequence of device-imparted supraphysiologic shear stresses, leading to shear-mediated platelet activation (SMPA). In advancing MCS devices from design to clinical use, in-vitro circulatory loops containing the device under development and testing are utilized as a means of assessing device thrombogenicity. Physical characteristics of these test circulatory loops may too contribute to inadvertent platelet activation through imparted shear stress, adding inadvertent error in evaluating MCS device thrombogenicity. While investigators normally control for the effect of a loop, inadvertent addition of what are considered innocuous connectors may impact test results. Here we tested the effect of common, additive components of in-vitro circulatory test loops, i.e. connectors and loop geometry, as to their additive contribution to shear stress via both in-silico and in-vitro models. A series of test circulatory loops containing a ventricular assist device (VAD) with differing constituent components, were established in-silico including: loops with 0 ~ 5 Luer connectors, a loop with a T-connector creating 90° angulation, and a loop with 90° angulation. Computational fluid dynamics (CFD) simulations were performed using a Ƙ-ω shear stress transport (SST) turbulence model to platelet activation index based on a power law model. VAD-operated loops replicating in-silico designs were assembled in-vitro and gel-filtered human platelets were recirculated within (1 h) and SMPA was determined. Results: CFD simulations demonstrated high shear being introduced at non-smooth regions such as edge-connector boundaries, tubing, and at Luer holes. Noticeable peaks' shifts of sss distributions towards high shear-region existed with increasing loop complexity. Platelet activation also increased with increasing shear exposure time, being statistically higher when platelets were exposed to connector-employed loop designs. The extent of platelet activation in-vitro could be successfully predicted by CFD simulations. Loops employing additional components (non-physiologically flow pattern connectors) resulted in higher platelet activation index. Loops with more components (5-connector loop and 90° T-connector) showed 63% and 128% higher platelet activation levels, respectively, versus those with fewer (0-connector (p=0.023) and a 90° heat-bend loop (p=0.0041). Our results underscore the importance of careful consideration of all component elements, and suggest the need for standardization, in designing in-vitro circulatory loops for MCS device evaluation to avoid inadvertent additive SMPA during device evaluation, confounding overall results. Specifically, we caution on the use and inadvertent introduction of additional connectors, ports and other shear-generating elements which introduce artifact, clouding primary device evaluation via introduction of additive SMPA.