Miracle-dz/UniFAR-FTUs huggingface dataset:
Analytical and diagnostic performance characteristics of reverse-transcriptase loop-mediated isothermal amplification assays for dengue virus serotypes 1–4: A scoping review to inform potential use in portable molecular diagnostic devices

Dengue is a mosquito-borne disease caused by dengue virus (DENV) serotypes 1–4 which affects 100–400 million adults and children each year. Reverse-transcriptase (RT) quantitative polymerase chain reaction (qPCR) assays are the current gold-standard in diagnosis and serotyping of infections, but their use in low-middle income countries (LMICs) has been limited by laboratory infrastructure requirements. Loop-mediated isothermal amplification (LAMP) assays do not require thermocycling equipment and therefore could potentially be deployed outside laboratories and/or miniaturised. This scoping literature review aimed to describe the analytical and diagnostic performance characteristics of previously developed serotype-specific dengue RT-LAMP assays and evaluate potential for use in portable molecular diagnostic devices. A literature search in Medline was conducted. Studies were included if they were listed before 4th May 2022 (no prior time limit set) and described the development of any serotype-specific DENV RT-LAMP assay (‘original assays’) or described the further evaluation, adaption or implementation of these assays. Technical features, analytical and diagnostic performance characteristics were collected for each assay. Eight original assays were identified. These were heterogenous in design and reporting. Assays’ lower limit of detection (LLOD) and linear range of quantification were comparable to RT-qPCR (with lowest reported values 2.2x101 and 1.98x102 copies/ml, respectively, for studies which quantified target RNA copies) and analytical specificity was high. When evaluated, diagnostic performance was also high, though reference diagnostic criteria varied widely, prohibiting comparison between assays. Fourteen studies using previously described assays were identified, including those where reagents were lyophilised or ‘printed’ into microfluidic channels and where several novel detection methods were used. Serotype-specific DENV RT-LAMP assays are high-performing and have potential to be used in portable molecular diagnostic devices if they can be integrated with sample extraction and detection methods. Standardised reporting of assay validation and diagnostic accuracy studies would be beneficial.
Distributional Functions are Crucial to Word Meaning : An Investigation of Semantic Associations

This article presents a study to distinguish and quantify the various types of semantic associations provided by humans, and to illustrate their usage for NLP purposes. Specifically, we address the task of modelling word meaning by empirical features in data-intensive lexical semantics. Relying on largescale corpus-based resources, we identify the contextual categories and functions that are activated by the associates and therefore contribute to the salient meaning components of individual words and established across words. As a result, we present prominent conceptual roles and evidence for the usefulness of co-occurrence information in distributional descriptions.
Integrated global analysis in spider flowers illuminates features underlying the evolution and maintenance of C4 photosynthesis

Abstract The carbon concentrating mechanism—C4 photosynthesis—represents a classic example of convergent evolution, but how this important trait originated and evolved remains largely enigmatic. The spider flower Gynandropsis gynandra is a valuable leafy vegetable crop and medicinal plant that has also been recognized as a C4 model species. Here we present a high-quality chromosome-scale annotated genome assembly of G. gynandra through a combination of Oxford Nanopore Technology (ONT), HiFi and Hi-C technology. The 17 super-scaffolds cover 98.66% of the estimated genome (997.61 Mb), with a contig N50 of 11.43 Mb and a scaffold N50 of 51.02 Mb. Repetitive elements occupy up to 71.91% of its genome, and over half are long terminal repeat retrotransposons (LTR-RTs) derived from recent bursts, contributing to genome size expansion. Strikingly, LTR-RT explosion also played a critical role in C4 evolution by altering expression features of photosynthesis-associated genes via preferential insertion in promoters. Integrated multiomics analyses of G. gynandra and the ornamental horticulture C3 relative Tarenaya hassleriana reveal that species-specific whole-genome duplication, gene family expansion, recent LTR–RT amplification, and more recent tandem duplication events have all facilitated the evolution of C4 photosynthesis, revealing uniqueness of C4 evolution in the Cleome genus. Moreover, high leaf vein density and heat stress resilience are associated with shifted gene expression patterns. The mode of C3-to-C4 transition found here yields new insights into evolutionary convergence of a complex plant trait. The availability of this reference-grade genomic resource makes G. gynandra an ideal model system facilitating efforts toward C4-aimed crop engineering.
Network Anomaly Detector System for Active Networks

Increasing attacks necessitates the need for an efficient intrusion system for mitigating such attacks. Anomaly detection among other types of Intrusion detection(ID) plays a vital role in Intrusion detection systems(IDS). The various IDS proposed in the literature, are not complete in detecting attacks to desired probability. In this paper a complete solution to anomaly detection of intrusions in the network is drafted. A two stage detection process is assumed where the IDS performs the common pattern detection using signatures in the first stage followed by an anomaly detector in the second stage. Focus is made only on the second stage in this paper to address anomaly detection. The detection is based on network traffic analysis with less monitoring overhead and is deployed in active networks. This paper attempts to define a complete anomaly detector utilising two novel algorithms namely packet marker algorithm and mutual path algorithm to provide an efficient and reliable solution for the anomaly detection whose implementation is underway and it is expected to provide better response in terms of false positive /negative prediction and delay in prediction.
Ex vivo expansion of lung cancer‐derived disseminated cancer cells from lymph nodes identifies cells associated with metastatic progression

The cellular basis of the apparent aggressiveness in lung cancer is poorly understood but likely associated with functional or molecular features of disseminated cancer cells (DCCs). DCCs from epithelial cancers are mostly detected by antibodies directed against histogenetic markers such as cytokeratin or EpCAM. It has been argued that marker‐negative metastatic founder cells might escape detection. We therefore used ex vivo sphere formation for functional detection of candidate metastasis founders. We generated cell suspensions from 199 LN samples of 131 lung cancer patients and placed them into non‐adherent cell culture. Sphere formation was associated with detection of DCCs using EpCAM immunocytology and with significantly poorer prognosis. The prognostic impact of sphere formation was strongly associated with high numbers of EpCAM‐positive DCCs and aberrant genotypes of expanded spheres. We also noted sphere formation in patients with no evidence of lymphatic spread, however such spheres showed infrequent expression of signature genes associated with spheres from EpCAM‐positive samples and displayed neither typical lung cancer mutations (KRAS, TP53, ERBB1) nor copy number variations, but might be linked to disease progression >5 years post curative surgery. We conclude that EpCAM identifies relevant disease‐driving DCCs, that such cells can be expanded for model generation and that further research is needed to clarify the functional and prognostic role of rare EpCAM‐negative sphere forming cells.
Speech Outcomes Audit for Unilateral Cleft lip and Palate After 2-Stage Palate Repair: Preliminary Results

Primary cleft lip and palate surgeries can interfere with speech status, facial appearance, maxillary growth, and psychosocial and academic development. Therefore, different surgical protocols and techniques have been proposed, and adequate velopharyngeal function and speech is the main goal for the treatment success. The present study aimed to report preliminary speech results of the 2-stage palate repair of children with unilateral cleft lip and palate. One hundred seventy nonsyndromic patients with unilateral cleft lip and palate were included in this report, 35% males and 65% females, submitted to the 2-stage palatoplasty protocol, composed by lip, nasal ala, and hard palate repair at 3 to 6 m (stage 1) and soft palate repair at 12 to 18 m (stage 2). The target age range for speech recording was 5 to 10 years, and the speech material included repetition of Brazilian Portuguese sentences. These samples were obtained over 5 years and assessed by 3 of 14 experienced speech pathologists. When discordant, the majority rate was adopted. Average velopharyngeal dysfunction (VPD) rates were 19,5%, varying according to the soft palate technique, with better results when the Sommerlad technique was performed (VPD=11%), followed by Braithwaite (VPD=15%) and then Von Langenbeck (VPD=25%). Passive errors were observed in 32% and active errors in 25%. Speech results reflect the outcomes of an interdisciplinary team’s work, where facial growth and nasolabial appearance must also be considered. Further analysis and a wider casuistic are recommended. Hence outcomes audit needs to be a permanent process, providing solid and updated evidence for optimal cleft care.
Enhanced bone regeneration using Antheraea mylitta silk fibroin and chitosan based scaffold: in-vivo and in-vitro study

In this study, highly interconnected porous scaffolds from Antheraea mylitta silk fibroin (SF) and chitosan (CH) were fabricated using the freeze-drying method. The weight ratios of SF to CH were varied from 90:10 (SF90/CH10) to 50:50 (SF50/CH50) to prepare the scaffolds from the aqueous suspension of the protein-polysaccharide mix. From the initial optimization of scaffold composition with respect to their microstructure, porosity, and mechanical properties, the SF80/CH20 scaffold exhibited the most suitable properties for bone tissue engineering application as compared to others compositions. Hence in-vitro hemocompatibility, protein adsorption, and MG-63 cell culture studies were carried out for SF80/CH20 scaffold. The fabricated SF80/CH20 scaffold showed a more controlled swelling percentage of 42.8%, with high BSA protein adsorption of 0.39 mg of BSA per gm of the scaffold at 24 h incubation period. Furthermore, in-vitro MG-63 cell culture study onto the fabricated SF80/CH20 scaffold elicited excellent MG-63 cell attachment with better biocompatibility and cell viability with increased F-action production from day 3 to day 7 of the cell culture period. In vivo bone defect healing in a rabbit tibia model revealed excellent bone healing capacity in SF80/CH20 scaffold implanted specimens compared to control ones, as evident from histology and fluorochrome labeling analysis.
Two-Year Clinical and Radiographic Outcomes for Percutaneous Lumbar Interbody Fusion With an Expandable Titanium Cage Through Kambin’s Triangle Without Facetectomy

Background There has been heightened interest in performing percutaneous lumbar interbody fusions (percLIFs) through Kambin’s triangle, an anatomic corridor allowing entrance into the disc space. However, due to its novelty, there are limited data regarding the long-term benefits of this procedure. Our objective was to determine the long-term efficacy and durability of the percutaneous insertion of an expandable titanium cage through Kambin’s triangle without facetectomy. Methods A retrospective review of patients undergoing percLIF via Kambin’s triangle using an expandable titanium cage was performed. Demographics, visual analog scale (VAS) scores, Oswestry Disability Index (ODI), radiographic measurements, perioperative variables, and complications were recorded. VAS, ODI, and radiographic measurements were compared with baseline using the generalized estimating equations assuming normally distributed data. Fusion was assessed with computed tomography (CT) at 1 and 2 years after the procedure. Results A total of 49 patients were included. Spondylolisthesis, lumbar lordosis (LL), sacral slope, pelvic tilt, and anterior/posterior disc space height were all significantly improved postoperatively at each time point of 3, 6, 12, and 24 months (P < 0.001). Pelvic incidence—LL mismatch decreased significantly at each follow-up (P < 0.001) with a mean reduction of 4° by 24 months. VAS back scores reduced by >2 points at the 6, 12, and 24 month follow-ups. ODI scores reduced by >15 points at the 12- and 24-month follow-ups. Of the patients who had 1- and 2-year CT images, fusion rates at those time points were 94.4% (17/18) and 87.5% (7/8), respectively. The mean annual rate of surgically significant adjacent segment disease was 2.74% through an average follow-up of 2.74 years. Conclusion These results highlight that percLIF, a procedure done without an endoscope or facetectomy, can be performed using an expandable titanium cage through Kambin’s triangle with excellent radiographic and clinical results. Clinical Relevance percLIF via Kambin’s triangle is a safe and succesful procedure with long-term improvements in both clinical and radiographic outcomes. Level of Evidence 3.
T-lymphocyte depleted transplants for inborn errors of immunity

ABSTRACT Introduction Hematopoietic stem cell transplantation is a curative treatment for many inborn errors of immunity (IEI). Incremental improvements and advances in care have led to high rates of >85% survival and cure in many of these diseases. Improvements in HLA-classification and matching have led to increased survival using HLA-matched donors, but survival using T-lymphocyte-depleted mismatched grafts remained significantly worse until fairly recently. Advances in T-lymphocyte depletion methods and graft engineering, although not specific to IEI, have been widely adopted and instrumental in changing the landscape of donor selection, such that a donor should now be possible for every patient. Areas covered A literature review focusing on T-lymphocyte depletion methodologies and treatment results was performed. The importance of early T-lymphocyte immunoreconstitution to protect against viral infection is reviewed. Two main platforms now dominate the field – immune-magnetic selection of specific cell types and post-transplant chemotherapeutic targeting of rapidly proliferating allo-reactive T-lymphocytes – the emerging literature on these reports, focusing on IEI, is explored, as well as the impact of serotherapy on early immunoreconstitution. Expert opinion Pharmacokinetic monitoring of serotherapy agents, and use of co-stimulatory molecule blockade are likely to become more widespread. Post-transplant cyclophosphamide or TCR depletion strategies are likely to become the dominant methods of transplantation for nonmalignant diseases.
Are current wound classifications valid for predicting prognosis in people treated for limb‐threatening diabetic foot ulcers?

Abstract This study aims to investigate whether the current wound classifications were valid for the treatment prognosis of subjects treated for limb‐threatening diabetic foot ulcers (LTDFU). A total of 1548 patients with LTDFU and infection were studied, with wounds recorded using the Wagner, Texas, PEDIS and WIfI classifications while major lower extremity amputations (LEAs) or in‐hospital mortality incidences were defined as poor outcomes. Among them, 153 (9.9%) patients received major LEAs and 38 (2.5%) patients died. After adjustments, the Wagner classification and Texas stage as well as clinical factors such as comorbidity with major adverse cardiac events (MACE), being under dialysis and having serum levels of C‐reactive protein (CRP) and albumin were independent factors for prognosis. For patients without dialysis, Wagner and Texas stage stood out independently for prognosis. For patients on dialysis, only levels of CRP (odds ratio [OR] = 2.2 in Wagner, OR = 2.0 in WIfI, OR = 2.2 in Texas, OR = 2.3 in PEDIS) and albumin (OR = 0.4 in four classifications) were valid predictors. The Wagner system and Texas stage were valid for predicting prognosis in treatment for LTDFUs, suggesting a role of vascular perfusion. MACE history, levels of CRP and albumin level should assist in prediction; more significantly, only levels of CRP and albumin appeared valid for those subjects undergoing dialysis.
RVE2, a new regulatory factor in jasmonic acid pathway, orchestrates resistance to Verticillium wilt

Summary Verticillium dahliae, one of the most destructive fungal pathogens of several crops, challenges the sustainability of cotton productivity worldwide because very few widely‐cultivated Upland cotton varieties are resistant to Verticillium wilt (VW). Here, we report that REVEILLE2 (RVE2), the Myb‐like transcription factor, confers the novel function in resistance to VW by regulating the jasmonic acid (JA) pathway in cotton. RVE2 expression was essentially required for the activation of JA‐mediated disease‐resistance response. RVE2 physically interacted with TPL/TPRs and disturbed JAZ proteins to recruit TPL and TPR1 in NINJA‐dependent manner, which regulated JA response by relieving inhibited‐MYC2 activity. The MYC2 then bound to RVE2 promoter for the activation of its transcription, forming feedback loop. Interestingly, a unique truncated RVE2 widely existing in D‐subgenome (GhRVE2D) of natural Upland cotton represses the ability of the MYC2 to activate GhRVE2A promoter but not GausRVE2 or GbRVE2. The result could partially explain why Gossypium barbadense popularly shows higher resistance than Gossypium hirsutum. Furthermore, disturbing the JA‐signalling pathway resulted into the loss of RVE2‐mediated disease‐resistance in various plants (Arabidopsis, tobacco and cotton). RVE2 overexpression significantly enhanced the resistance to VW. Collectively, we conclude that RVE2, a new regulatory factor, plays a pivotal role in fine‐tuning JA‐signalling, which would improve our understanding the mechanisms underlying the resistance to VW.
Diet Preference and Prey of Olive Ridley Turtles (Lepidocheyls olivacea) along East Coast of India, Odisha

This study was made on gut content of 182 dead wash ashore olive ridley turtles, (56 sub-adults, and 126 adult) of which 77, 100 and 5 guts were from Gahirmatha, Devi and Rushikulaya respectively. Autopsy was done during the breeding seasons of February 2008 to April 2010 at Odisha coast on three arribada beaches of the world. To identify the food preference of Olive ridley volumetric and frequency of occurrence percent was calculated. Gut content of turtles was segregated into four size class based on curve carapace length (CCL) ( 80cm) and classified into two groups sub-adult and adult. In total 88.15% was of animal prey 6.65% of volume was plant. Although there was no significant difference within two size class of the sub-groups, sub adult and adult. But the diet differs significantly in adult and sub adult group. On analyzing the diet through Percent similarity index among the size class of turtles the most preferred phyla of prey items taken was Mollusca which add 30% of volume in food to all size class of turtles with highest diversity of 12 families and Muricidae family gave more prey item in invertebrate.
Low‐frequency oscillometry indices to assess ventilation inhomogeneity in CF patients

The utility of the forced oscillations technique (FOT) in cystic fibrosis (CF) remains uncertain. The aim of this study was to explore the ability of lower‐frequency FOT indices, alone and after adjustment for the lung volume, to assess the extent of ventilation inhomogeneity in CF patients with varying disease severity.
Abdominal access in laparoscopic surgery of obese patients: a novel abdominal access technique

BACKGROUND: An important step in laparoscopic surgery is abdominal access. Several abdominal access techniques have been described to reduce complications. We compare our novel abdominal access technique (MESAD) with other abdominal access techniques, particularly to reduce complications in obese patients. OBJECTIVE: Compare the MESAD method and other methods we use for abdominal access in gynecologic laparoscopic surgery of obese patients DESIGN: Retrospective SETTING: Gynecology department in university hospital PATIENTS AND METHODS: Patients who underwent abdominal access by the MESAD technique, the Veress needle technique, and the Hasson technique were included in our study. In addition to demographic data, minor and major complications, number of unsuccessful attempts, conversion to another technique, and abdominal access times were collected from all patient files. MAIN OUTCOME MEASURES: Clinical data and complications SAMPLE SIZE: 66 patients, 26 by MESAD technique, 24 by the Veress needle technique, and 16 by the Hasson technique. RESULTS: There were two major complications (one in the Veress group and one in the Hasson technique group) and 7 minor complications. No significant difference was found between the groups in terms of complications (P=.477, P=.476, respectively). The fastest technique for abdominal access was in the MESAD technique whereas the slowest was in the Hasson (P<.001). The failure of abdominal access and subsequent conversion to another technique was most common in the Veress group. However, no significant difference was found between the groups (P=.092). CONCLUSIONS: The MESAD technique is an easy method to both learn and teach. We think that the low major-minor complication rates in the MESAD technique will allow surgeons to reduce their anxiety at the first entry and to perform a more comfortable operation. LIMITATIONS: Retrospective CONFLICT OF INTEREST: None.