Miracle-dz/UniFAR-FTUs huggingface dataset:
Association between plasma complement factor H concentration and clinical outcomes in patients with sepsis

The complement system is important for defending against pathogens, however, excessive complement activation is associated with a poor prognosis and organ dysfunction in sepsis. Complement factor H (CFH) acts to prevent excessive complement activation and damage to the self through the regulation of the complement alternative pathway. We investigated the association between plasma CFH levels on admission to the intensive care unit (ICU) and 90‐day mortality, severity scores, and organ dysfunction in patients with sepsis.
Handheld Point-of-Care System for Rapid Detection of SARS-CoV-2 Extracted RNA in under 20 min

The COVID-19 pandemic is a global health emergency characterized by the high rate of transmission and ongoing increase of cases globally. Rapid point-of-care (PoC) diagnostics to detect the causative virus, SARS-CoV-2, are urgently needed to identify and isolate patients, contain its spread and guide clinical management. In this work, we report the development of a rapid PoC diagnostic test (<20 min) based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) and semiconductor technology for the detection of SARS-CoV-2 from extracted RNA samples. The developed LAMP assay was tested on a real-time benchtop instrument (RT-qLAMP) showing a lower limit of detection of 10 RNA copies per reaction. It was validated against extracted RNA from 183 clinical samples including 127 positive samples (screened by the CDC RT-qPCR assay). Results showed 91% sensitivity and 100% specificity when compared to RT-qPCR and average positive detection times of 15.45 ± 4.43 min. For validating the incorporation of the RT-LAMP assay onto our PoC platform (RT-eLAMP), a subset of samples was tested (n = 52), showing average detection times of 12.68 ± 2.56 min for positive samples (n = 34), demonstrating a comparable performance to a benchtop commercial instrument. Paired with a smartphone for results visualization and geolocalization, this portable diagnostic platform with secure cloud connectivity will enable real-time case identification and epidemiological surveillance.
Effective ribosomal RNA depletion for single-cell total RNA-seq by scDASH

A decade since its invention, single-cell RNA sequencing (scRNA-seq) has become a mainstay technology for profiling transcriptional heterogeneity in individual cells. Yet, most existing scRNA-seq methods capture only polyadenylated mRNA to avoid the cost of sequencing non-messenger transcripts, such as ribosomal RNA (rRNA), that are usually not of-interest. Hence, there are not very many protocols that enable single-cell analysis of total RNA. We adapted a method called DASH (Depletion of Abundant Sequences by Hybridisation) to make it suitable for depleting rRNA sequences from single-cell total RNA-seq libraries. Our analyses show that our single-cell DASH (scDASH) method can effectively deplete rRNAs from sequencing libraries with minimal off-target non-specificity. Importantly, as a result of depleting the rRNA, the rest of the transcriptome is significantly enriched for detection.
GAMATCH : a genetic algorithm-based program for indexing crystal faces

An intelligent genetic algorithm-based crystal-indexing program, GAMATCH, is described, by means of which the Miller indices of the relevant planes can be unambiguously identified using a set of interplanar angles. A two-step-divide-and-conquer strategy is employed and is found to speed up the convergence to the global solution. The program was tested using both hypothetical and centimetre-sized triphenylmethyl chloride crystals. The results obtained were compared to the expected indices and excellent agreement was noted.
Anesthetic Considerations for Transcarotid Artery Revascularization: Experience and Review of Forty Cases From a Single Medical Center

Transcarotid artery revascularization (TCAR) procedure is a novel hybrid surgical modality in treating carotid stenosis. Understanding the various steps of the TCAR and the unique challenges involved in the anesthetic management is essential for the successful conduct of anesthesia. In this article, we discuss the overview of the key issues relevant to the anesthetic management and strategies from our experience. We present the data on anesthetic management and outcomes of 40 patients who underwent TCAR procedure at our institute between June 2018 and February 2020. Electronic medical records were retrospectively reviewed and relevant demographic, clinical, and laboratory data were collected. All our patients had general anesthesia with an endotracheal tube utilizing standard American Society of Anesthesiology (ASA) monitoring along with intra-arterial blood pressure monitoring and cerebral oximetry. The mean age of our patients was 73.6 ± 7.58 years. Fifteen (37.5 %) patients had significant co-morbidities, thus classified as ASA 4 and 10 (25%) patients were on at least three antihypertensives (beta-blockers, calcium channel blockers, angiotensin-converting enzyme inhibitors, loop diuretics, thiazides). Thirty-four (85%) patients were considered to have symptomatic carotid stenosis which was the predominant indication for the TCAR procedure. Patients who had episodes of transient ischemic attack (TIA) or a cerebrovascular accident (CVA) documented by a computerized tomography (CT) scan of the brain and/or residual weakness are considered symptomatic. Thirty-six (90%) of our patients received a bolus dose of 0.2 - 0.4 mg of glycopyrrolate for maintaining heart rate of around 70 beats per minute (BPM) and 38 (95%) received phenylephrine infusion during the carotid clamp to maintain blood pressure between 140 and 160 mm Hg systolic or at patients’ baseline. Twenty-one (52.5%) patients needed antihypertensives such as hydralazine ( 10-20 mg) or beta-blockers such as labetalol (10-20 mg) at the time of emergence from anesthesia to mitigate hemodynamic response during extubation. The mean blood loss was 74 ml ± 33.19 ml, and none of our patients received blood transfusion during the perioperative period. The mean duration of anesthesia was 202.6 ± 27.85 minutes, and the mean length of hospital stay was 1.5 ± 0.97 days. A thorough preoperative examination with specific attention to the preoperative neurological deficits and cardiopulmonary reserve is important for the meticulous management of intraoperative hemodynamics. Intraoperative administration of glycopyrrolate and the use of vasopressors to maintain optimal hemodynamics to ensure cerebral perfusion during the perioperative period should be considered. The anesthetic goals of carotid revascularization (TCAR) are perioperative hemodynamic stability and early evaluation of neurological status in the immediate postoperative period.
High expression of MAPK-14 promoting the death of chondrocytes is an important signal of osteoarthritis process

Background Osteoarthritis (OA) is one of the most common degenerative diseases worldwide. Many researchers are studying the pathogenesis of OA, however, it is still unclear. Methods Screening and validation of OA relevant hub genes are an important part of exploring their potential molecular mechanism. Therefore, this study aims to explore and verify the mechanisms of hub genes in the OA by bioinformatics, qPCR, fluorescence and propidium iodide staining. Results Microarray datasets GSE43923, GSE55457 and GSE12021 were collected in the Gene Expression Omnibus (GEO), including 45 samples, which divided into 23 osteoarthritis knee joint samples and 22 samples of normal knee joint. Thereafter, 265 differentiallyexpressedgenes (DEGs) were identified in all, which divided into 199 upregulated genes and 66 downregulated genes. The hub genes MAPK-14, PTPRC, PTPN12 were upregulated, while B9D1 was downregulated. In order to further confirm the expression of screening differential genes in human chondrocytes, the human chondrocytes were extracted from a joint replacement surgery and stained with toluidine blue for identification. Compared with normal chondrocytes, OA chondrocytes had high expression of COL I protein and low expression of COL II protein. The expression levels of MAPK-14, PTPRC and PTPN12 in OA chondrocytes were significantly higher than the expression levels of B9D1 in normal chondrocytes. Moreover, the inflammatory necrosis of OA chondrocytes was increased compared with the normal chondrocytes by propidium iodide staining. Conclusions The high expression of MAPK-14 works as a promoter of chondrocytes death and an important signal of the osteoarthritis process.
The Antioxidant and Anti-Inflammatory Effects of Quercus brantii Extract on TNBS-Induced Ulcerative Colitis in Rats

Objectives Ulcerative colitis is a common subtype of persistent inflammatory bowel disease with high morbidity consequences. Despite unknown definite pathogenesis, multiple anti-inflammatory medications are used for its treatment. Traditionally, Quercus brantii (QB), mostly available in the Middle East, has been used for gastrointestinal disorders. Other beneficial effects associated with QB include reduction of oxidative stress, inflammations, homeostatic instability, and improvement in clinical conditions. Materials and Methods This experimental study was designed to assess the possible therapeutic effects of QB on UC and compare its effects with those of sulfasalazine. Of the 70 Wistar rats clustered in seven groups, ten received only alcohols and sixty were confirmed to be suffering from trinitrobenzene sulfonic acid- (TNBS-) induced colitis. Four groups received different dosages of QB extract via oral and rectal routes, one received sulfasalazine, and the other remaining two groups received nothing. The effects of QB were evaluated by assessing macroscopic and histologic scoring, measuring inflammatory mediators, and determining oxidative stress markers. Results Comparing to the untreated TNBS-induced control groups, QB-treated groups showed a dose- and route-dependent improvement comparable with sulfasalazine. Treating rats with QB reduced the microscopic and macroscopic damage, decreased TNF-α, IL-6, NO, MPO activity, and MDA content, increased superoxide dismutase (SOD) activity, and reduced body weight loss. Conclusions Our data recommended the anti-inflammatory and antioxidant effects of QB extract in a dose-dependent manner.
Effective immune-inﬂammation index for ulcerative colitis and activity assessments

BACKGROUND The inverse association between systemic immune-inﬂammation index (SII) and overall survival in tumors has been studied. AIM To evaluate the hematological indexes for assessing the activity of ulcerative colitis (UC). METHODS In this case-control study, 172 UC patients and healthy participants were included. Comparisons were made among groups of white blood cells, hemoglobin, platelets, neutrophils, lymphocytes, monocytes, SII, neutrophil-to-lymphocyte ratio (NLR), and platelet-to-lymphocyte ratio (PLR). The relationship with hematological inflammation was verified by Spearman correlation analyses. The efficiency of SII, NLR, and PLR for distinguishing between UC and severe disease status was assessed by the receiver operator curve and logistic regression analyses. RESULTS The values of SII, NLR, and PLR were higher in UC patients than in controls (P < 0.001) and were positively correlated with the Mayo endoscopic score, extent, Degree of Ulcerative Colitis Burden of Luminal Inflammation (DUBLIN) score, and Ulcerative Colitis Endoscopic Index of Severity (UCEIS). The cut-off NLR value of 562.22 predicted UC with a sensitivity of 79.65% and a specificity of 76.16%. Logistic regression analysis revealed that patients with SII and NLR levels above the median had a significantly higher risk of UC (P < 0.05). Risk factors independently associated with DUBLIN ≥ 3 included SII ≥ 1776.80 [odds ratio (OR) = 11.53, P = 0.027] and NLR value of 2.67-4.23 (OR = 2.96, P = 0.047) on multivariate analysis. Compared with the first quartile, SII ≥ 1776.80 was an independent predictor of UCEIS ≥ 5 (OR = 18.46, P = 0.012). CONCLUSION SII has a certain value in confirming UC and identifying its activity.
Rupture of rubber. I. Characteristic energy for tearing

The resistance to tearing of a rubber vulcanizate is usually determined by loading in a specified manner a test-piece of the vulcanizate of standard shape, in which a notch has been produced, either in the molding process or by cutting the test-piece in a standard fashion. A wide variety of shapes of test-piece and notch and of methods of loading have been recommended by various authors (see, for example, Buist1).
Thermodynamic and structural properties of Yukawa hard chains

The thermodynamic and structural properties of Yukawa hard chains are considered in this work. We specifically examined the influence of the Yukawa potential range parameter λ on the thermodynamic properties, inter- and intrachain correlation functions of the chain fluid. The compressibility factor or pressure of Yukawa chain fluids was calculated via a first-order perturbation theory using hard-sphere chain fluid as a reference. Monte Carlo simulations were performed to calculate the thermodynamic properties and inter- and intrachain correlation functions of the fluid for λ=1.8 and 3.0. Simulation results for the compressibility were compared with calculations from the first-order perturbation theory and the Statistical Associating Fluid Theory-Variable Range (SAFT-VR) model. We found that both theories represent the simulated data very well. In particular, the SAFT-VR equation provides an excellent estimate of the properties of Yukawa hard chains over wide ranges of temperature and density. Simulated da.
The complete chloroplast genome of Syzygium acuminatissimum

Abstract Syzygium acuminatissimum is a valuable hard wood species in southern China. In this study, we sequenced, assembled and annotated the complete chloroplast genome of S. acuminatissimum. The complete cp genome of S. acuminatissimum was 159,352 bp in length, with a total of 109 unique annotated genes, including 78 protein-coding genes, 27 tRNA genes and 4 rRNA genes. Phylogenetic analysis showed that S. acuminatissimum was closely related to its congener S. aromaticum.
Cryphonectriaceae associated with rust-infected Syzygium jambos in Hawaii

Abstract Syzygium jambos (Myrtales, Myrtaceae) trees in Hawaii are severely affected by a rust disease caused by Austropuccinia psidii (Pucciniales, Sphaerophragmiaceae), but they are commonly co-infected with species of Cryphonectriaceae (Diaporthales). In this study, S. jambos and other trees in the Myrtales were examined on three Hawaiian Islands for the presence of Cryphonectriaceae. Bark samples with fruiting bodies were collected from infected trees and fungi were isolated directly from these structures. Pure cultures were produced and the fungi were identified using DNA sequence data for the internal transcribed spacer (ITS) region, part of the β-tubulin (BT1) gene and the transcription elongation factor-1α (TEF1) gene. Five species in three genera of Cryphonectriaceae were identified from Myrtaceae tree samples. These included Chrysoporthe deuterocubensis, Microthia havanensis and three previously-unknown taxa described here as Celoporthe hauoliensis sp. nov., Cel. hawaiiensis sp. nov. and Cel. paradisiaca sp. nov. Representative isolates of Cel. hauoliensis, Cel. hawaiiensis, Cel. paradisiaca, Chr. deuterocubensis and Mic. havanensis were used in artificial inoculation studies to consider their pathogenicity on S. jambos. Celoporthe hawaiiensis, Cel. paradisiaca and Chr. deuterocubensis produced lesions on young S. jambos trees in inoculation trials, suggesting that, together with A. psidii, they may contribute to the death of trees. Microsatellite markers were subsequently used to consider the diversity of Chr. deuterocubensis on the Islands and thus to gain insights into its possible origin in Hawaii. Isolates of this important Myrtaceae and particularly Eucalyptus pathogen were found to be clonal. This provides evidence that Chr. deuterocubensis was introduced to the Hawaiian Islands as a single introduction, from a currently unknown source.
Identification and molecular characterization of mutations in nucleocapsid phosphoprotein of SARS-CoV-2

SARS-CoV-2 genome encodes four structural proteins that include the spike glycoprotein, membrane protein, envelope protein and nucleocapsid phosphoprotein (N-protein). The N-protein interacts with viral genomic RNA and helps in packaging. As SARS-CoV-2 spread to almost all countries worldwide within 2–3 months, it also acquired mutations in its RNA genome. Therefore, this study was conducted with an aim to identify the variations present in N-protein of SARS-CoV-2. Here, we analysed 4,163 reported sequence of N-protein from United States of America (USA) and compared them with the first reported sequence from Wuhan, China. Our study identified 107 mutations that reside all over the N-protein. Further, we show the high rate of mutations in intrinsically disordered regions (IDRs) of N-protein. Our study show 45% residues of IDR2 harbour mutations. The RNA-binding domain (RBD) and dimerization domain of N-protein also have mutations at key residues. We further measured the effect of these mutations on N-protein stability and dynamicity and our data reveals that multiple mutations can cause considerable alterations. Altogether, our data strongly suggests that N-protein is one of the mutational hotspot proteins of SARS-CoV-2 that is changing rapidly and these mutations can potentially interferes with various aspects of N-protein functions including its interaction with RNA, oligomerization and signalling events.
The Rise of Inflow Cisternostomy in Resource-Limited Settings: Rationale, Limitations, and Future Challenges

Low- and middle-income countries (LMICs) bear most of the global burden of traumatic brain injury (TBI), but they lack the resources to address this public health crisis. For TBI guidelines and innovations to be effective, they must consider the context in LMICs; keeping this in mind, this article will focus on the history, pathophysiology, practice, evidence, and implications of cisternostomy. In this narrative review, the author discusses the history, pathophysiology, practice, evidence, and implications of cisternostomy. Cisternostomy for the management of TBI is an innovation developed in LMICs, primarily for LMICs. Its practice is based on the cerebrospinal fluid shift edema theory that attributes injury to increased pressure within the subarachnoid space due to subarachnoid hemorrhage and subsequent dysfunction of glymphatic drainage. Early reports of the technique report significant improvements in the Glasgow Outcome Scale, lower mortality rates, and shorter intensive care unit durations. Most reports are single-center studies with small sample sizes, and the technique requires experience and skill. These limitations have led to criticisms and slow adoption of the technique. Further research is needed to establish the effect of cisternostomy on TBI outcomes.
妊娠合并淋巴瘤患者的管理

Management of patients with lymphoma in pregnancy Wang Huifang, Liang Meiying, Jiang Qian Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China; Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing 100044, China Corresponding author: Jiang Qian, Email: jiangqian@medmail.com. cn; Liang Meiying, Email: lmying1129@163.com
Choroid Segmentation of Retinal OCT Images Based on CNN Classifier and l2-lq Fitter

Optical coherence tomography (OCT) is a noninvasive cross-sectional imaging technology used to examine the retinal structure and pathology of the eye. Evaluating the thickness of the choroid using OCT images is of great interests for clinicians and researchers to monitor the choroidal thickness in many ocular diseases for diagnosis and management. However, manual segmentation and thickness profiling of choroid are time-consuming which lead to low efficiency in analyzing a large quantity of OCT images for swift treatment of patients. In this paper, an automatic segmentation approach based on convolutional neural network (CNN) classifier and l2-lq (0 < q < 1) fitter is presented to identify boundaries of the choroid and to generate thickness profile of the choroid from retinal OCT images. The method of detecting inner choroidal surface is motivated by its biological characteristics after light reflection, while the outer chorioscleral interface segmentation is transferred into a classification and fitting problem. The proposed method is tested in a data set of clinically obtained retinal OCT images with ground-truth marked by clinicians. Our numerical results demonstrate the effectiveness of the proposed approach to achieve stable and clinically accurate autosegmentation of the choroid.
The reliability and validity of the weight-bearing lunge test in a Congenital Talipes Equinovarus population (CTEV)

Question What is the intra and inter-rater reliability and concurrent validity of the weight-bearing lunge test within a Congenital Talipes Equinovarus population? Design Test retest design for reliability and validity. The measure was taken, following preconditioning of the participants, using distance from wall, angle at distal posterior tibia using a digital inclinometer and the iPhone level function, twice by each rater. The raters included a clinician, clinician in training and a parent/carer. Outcome measures Weight bearing lunge test as a measure of ankle dorsiflexion. Results Twelve children aged 5–10 years were eligible to participate and consented, along with their parents. Intra-reliability of distance measures for all raters were good to excellent (ICC clinician 0.95, ICC training clinician 0.98 and ICC parent 0.89). Intra-rater reliability of the iPhone for all raters was good (ICCs > 0.751) and good to excellent for the inclinometer (ICC clinician 0.87, ICC training clinician 0.90). Concurrent validity between the clinician’s and parents distance measure was also high with ICC of 0.899. Inter-rater reliability was excellent for distance measure (ICC = 0.948), good for the inclinometer (ICC = 0.801) and moderate for the iPhone (ICC = 0.68). Standard error of measurement ranged from 0.70–2.05, whilst the minimal detectable change ranged from 1.90–5.70. Conclusion The use of the WBLT within this CTEV population has demonstrated good to excellent reliability and validity amongst clinicians, clinicians in training and parents/carers, supporting its use as an assessment measure of dorsiflexion range of motion. There is support for parents/carers to use the WBLT at home as a monitoring assessment measure which may assist with early detection of a relapse. Trial registration University of South Australia’s ethics committee (ID: 201397); Women’s and Children’s Hospital ethics committee (AU/1/4BD7310).