Miracle-dz/UniFAR-FTUs huggingface dataset:
Epidemiology Characteristics of Streptococcus pneumoniae From Children With Pneumonia in Shanghai: A Retrospective Study

Background: Streptococcus pneumoniae is the most common pathogen causing death in children under 5 years old. This retrospective surveillance aimed to analyze serotype distribution, drug resistance, virulence factors, and molecular characteristics of pneumonia isolates from children in Shanghai, China. Methods: A total of 287 clinical pneumococcal isolates were collected from January to December in 2018 and were divided into community-acquired pneumonia (CAP) and healthcare-associated pneumonia (HAP) two groups according to where someone contracts the infection. All isolates were serotyped by multiplex sequential PCR and antimicrobial susceptibility testing was performed using E-test or disk diffusion method. The molecular epidemiology was analyzed using multilocus sequence typing and seven housekeeping genes were sequenced to identified the sequence types (STs). In addition, we investigated the presence of virulence genes via PCR. Results: The most common serotypes were 19F, 6A, 19A, 23F, 14, and 6B, and the coverage rates of the 7-, 10- and 13-valent pneumococcal conjugate vaccines were 58.9, 58.9, and 80.5%, respectively. More PCV13/non-PCV7 serotypes and higher rate of penicillin non-susceptible S. pneumoniae were seen in HAP. Molecular epidemiological typing showed a high level of diversity and five international antibiotic-resistant clones were found, including Taiwan19F-14, Spain23F-1, Spain6B-2, Taiwan23F-15 and Sweden15A-25. No significant difference was observed in the presence of virulence genes among the isolates obtained from CAP and HAP. All of the S. pneumoniae isolates carried lytA, ply, psaA, pavA, spxB, htrA, and clpP, and the carriage rate of nanA and piaA were 96.2 and 99.0%. Conversely, cps2A, cbpA, and pspA were present in 33.8–44.3% of the isolates. Conclusions: Serotype changes and emerging multidrug-resistant international clones were found in current study. lytA, ply, psaA, pavA, spxB, htrA, and clpP may be good protein vaccine candidates. Long-term high-quality surveillance should be conducted to assess impact and effectiveness brought by vaccines, and provide a foundation for prevention strategies and vaccine policies.
The Surgical Intervention for Traumatic Injury Scale: A Clinical Tool for Traumatic Brain Injury

Introduction There is no widely used method for communicating the possible need for surgical intervention in patients with traumatic brain injury (TBI). This study describes a scoring system designed to communicate the potential need for surgical decompression in TBI patients. The scoring system, named the Surgical Intervention for Traumatic Injury (SITI), was designed to be objective and easy to use. Methods The SITI scale uses radiographic and clinical findings, including the Glasgow Coma Scale Score, pupil examination, and findings noted on computed tomography. To examine the scale, we used the patient database for the Progesterone for the Treatment of Traumatic Brain Injury III (ProTECT III) trial, and retrospectively applied the SITI scale to these patients. Results Of the 871 patients reviewed, 164 (18.8%) underwent craniotomy or craniectomy, and 707 (81.2%) were treated nonoperatively. The mean SITI score was 5.1 for patients who underwent surgery and 2.5 for patients treated nonoperatively (P<0.001). The area under the receiver operating characteristic curve was 0.887. Conclusion The SITI scale was designed to be a simple, objective, clinical decision tool regarding the potential need for surgical decompression after TBI. Application of the SITI scale to the ProTECT III database demonstrated that a score of 3 or more was well associated with a perceived need for surgical decompression. These results further demonstrate the potential utility of the SITI scale in clinical practice.
Corneal Curvature: the Influence of Corneal Accommodation and Biomechanics on Corneal Shape

Purpose Variation in the presence and magnitude of corneal conformational changes during accommodation may predict postoperative ectasia following refractive surgery and assist in the early diagnosis of corneal ectatic disorders. The current study aimed to establish a baseline for corneal refractive changes during ocular accommodation and to clarify the role of biomechanical factors in predicting these changes in a population without corneal pathology. Methods GALILEI G2 corneal tomography was assessed in 63 participants in both the accommodated and unaccommodated states. Four diopters (D) of physiological accommodation were induced using near-acuity calibrated words viewed through an externally mounted beam splitter mounted on a three-dimensional-printed frame. Corneal biomechanical characteristics were assessed with the CorVis-ST instrument, and statistical analysis was completed in R software. Results Anterior chamber depth was reduced by 0.10 ± 0.07 mm with accommodation (P < 0.01). Areas of statistically significant change in corneal curvatures were seen in all participants with accommodation. Mean anterior instantaneous corneal power increased in the superior-nasal periphery (0.1 D, 95% confidence interval [CI] = 0.05–0.2 D) and decreased in the inferior-temporal periphery (0.1 D, 95% CI = −0.05 to −0.15 D). Corneal stiffness and the corneal deformation amplitude ratio predicted peripheral corneal curvature changes with accommodation (P < 0.05). Conclusion Corneal conformational changes occur during accommodation in normal subjects. Further studies are required to assess the magnitude of corneal changes during accommodation in patients with corneal ectasia. Translational Relevance An externally mounted beam splitter can be used to modify the visual target presented by clinical ocular imaging instruments. Corneal conformational changes during accommodation may be useful in the diagnosis of corneal ectasia.
The effect of deafness on the physical fitness parameters of elite athletes

The purpose of this study is to determine the health-related physical fitness parameters of athletes, who are deaf. The study group consisted of 137 deaf athletes (52 females and 85 males with a mean age of 23.99±6.56 years) who have participated in the 2017 Deaflympics games. The assessed parameters included the isokinetic muscle strength, core endurance, balance assessments, grip strength, and body composition. At the end of the study, the following results were obtained. Hamstring/quadriceps ratio was in the range of 53%–54%, which was within 50%–60% of the normal limit. Endurance of the anterior and posterior core muscles was low as compared to the normative data. The athletes’ balance was better with their eyes open than closed; and the grip strength was low as compared to the normative data in the literature. Also, the body fat percentage of deaf female athletes were similar to ones in healthy individuals with sedentary lifestyle, whereas male ones had slightly lower body fat mass percentage. These results can be used as the initial reference parameters to define the training program requirements of deaf athletes.
‘Mini-interval gait’ switching: understanding the positive implications of a novel training regime

The neuromechanical reorganization required to change gaits imposes an energetic cost 75% greater than either a walking or running step at the same speed. By combining walking and running with the requisite gait switching transition steps, an exercise protocol can be generated with virtually any desired metabolic output even at relatively slow treadmill speed. Gait switching increases metabolic demand through discrete events, which can be tolerated more easily by individuals recovering from health problems, just as interval training allows greater work production for healthy individuals. In addition to cardio-respiratory benefits, ‘mini-intervals’ with frequent gait switching also provides positive effects and attributes such as distributing muscle group activation, re-training neural coordination, and avoiding repetitive joint overloading. It has the added benefit of developing stability during transitions while a safety hand rail is present which can lead to greater stability in more complex natural environments. Finally, increased mental focus may help avoid the monotony of usual treadmill workouts, aiding adherence to an exercise program. We review evidence for the cost increase of the gait transition step and explain the mechanisms involved. We also discuss literature supporting the range of benefits for mini-interval gait switching as a training and rehabilitation tool.
Whole-Genome Resequencing Reveals Loci Associated With Thoracic Vertebrae Number in Sheep

The number of vertebrae, especially thoracic vertebrae, is an important economic trait that may influence carcass length and meat production in animals. However, the genetic basis of vertebrae number in sheep is still poorly understood. To detect the candidate genes, 400 increased number of thoracic vertebrae (T14L6) and 200 normal (T13L6) Kazakh sheep were collected. We generated and sequenced 60 pools of genomic DNA (each pool prepared by mixing genomic DNA from 10 sheep with the same thoracic traits), with an average depth of coverage of 25.65×. We identified a total of 42,075,402 SNPs and 11 putatively selected genomic regions, including the VRTN gene and the HoxA gene family that regulate vertebral development. The most prominent areas of selective elimination were located in a region of chromosome 7, including VRTN, which regulates spinal development and morphology. Further investigation indicated that the expression level of the VRTN gene during fetal development was significantly higher in sheep with more thoracic vertebrae than in those with a normal number of thoracic vertebrae. A genome-wide comparison between sheep with increased and normal numbers of thoracic vertebrae showed that the VRTN gene is the major selection locus for the number of thoracic vertebrae in sheep and has the potential to be utilized in sheep breeding in the future.
Reversible Watermarking Algorithm Based on Difference Expansion for 2D Engineering Drawings

In order to take effective copyright protection for 2D engineering drawings,the paper presents a reversible watermark embedding algorithm based on difference expansion for 2D engineering drawings.The algorithm works on the feature of poor relevant of vertex coordinates of lines in engineering drawing,embedding watermark information by modifying the vertex coordinates of lines.Because of minute revision,there isn't any visual redundancy.During information extracting,the algorithm can restore the original engineering drawing accurately,and meets the requirements of high-precision machining,and also realizes the blind extraction.The experimental results show that the algorithm achieves good results,and easy to implement,it can be applied to the copyright protection of engineering drawings,content certification,information secret transmission and other fields.
Human Urban Arboviruses Can Infect Wild Animals and Jump to Sylvatic Maintenance Cycles in South America

The present study shows that the most prominent human arboviruses worldwide (dengue viruses 1, 2, 3, and 4, Chikungunya virus, and Zika virus) can infect wild animals and transfer from urban to sylvatic maintenance cycles in South America, as did the yellow fever virus (YFV) in the past. All these viruses are transmitted by the anthropophilic mosquito Aedes aegypti and cause epidemics throughout Brazil. The YFV is the oldest example of an urban arbovirus that became sylvatic in South America. Currently, the disease is a zoonosis of non-human primates that moves like a wave through the forests of the Brazilian countryside, traveling thousands of kilometers, killing many animals and eventually infecting man. However, since 2016, this zoonotic wave has reached the highly populated areas of Southeast Brazil, producing the largest human outbreak in the past 60 years. As with the YFV, sylvatic cycles may occur with dengue, Chikungunya, and Zika. In order to become sylvatic, arboviruses require an apparently unlikely conjunction of factors to unexpectedly take place. These arboviruses could start to infect sylvatic primates and be transmitted by Haemagogus mosquitoes that inhabit tree canopies. We mention here publications reporting evidence of sylvatic cycles of dengue, Chikungunya, and Zika virus in South America. Indeed, it is almost unfeasible to control these cycles of arboviruses since it is impossible to know where, when or why an arboviral spill-over would occur in wild animals. The sylvatic maintenance cycle could preclude the eradication of an arbovirus. Moreover, an arbovirus in a sylvatic cycle could re-emerge anytime, infecting humans and producing outbreaks. In case of the reemergence of an arbovirus, it is crucial to prevent the occurrence of an urban cycle as a spill-back from the sylvatic cycle.
A Mathematical Model for the Hydrogenotrophic Metabolism of Sulphate-Reducing Bacteria

Sulphate-reducing bacteria (SRB) are studied across a range of scientific fields due to their characteristic ability to metabolise sulphate and produce hydrogen sulphide, which can lead to significant consequences for human activities. Importantly, they are members of the human gastrointestinal microbial population, contributing to the metabolism of dietary and host secreted molecules found in this environment. The role of the microbiota in host digestion is well studied, but the full role of SRB in this process has not been established. Moreover, from a human health perspective, SRB have been implicated in a number of functional gastrointestinal disorders such as Irritable Bowel Syndrome and the development of colorectal cancer. To assist with the study of SRB, we present a mathematical model for the growth and metabolism of the well-studied SRB, Desulfovibrio vulgaris in a closed system. Previous attempts to model SRB have resulted in complex or highly specific models that are not easily adapted to the study of SRB in different environments, such as the gastrointestinal tract. We propose a simpler, Monod-based model that allows for easy alteration of both key parameter values and the governing equations to enable model adaptation. To prevent any incorrect assumptions about the nature of SRB metabolic pathways, we structure the model to consider only the concentrations of initial and final metabolites in a pathway, which circumvents the current uncertainty around hydrogen cycling by SRB. We parameterise our model using experiments with varied initial substrate conditions, obtaining parameter values that compare well with experimental estimates in the literature. We then validate our model against four independent experiments involving D. vulgaris with further variations to substrate availability. Further use of the model will be possible in a number of settings, notably as part of larger models studying the metabolic interactions between SRB and other hydrogenotrophic microbes in the human gastrointestinal tract and how this relates to functional disorders.
Cytotoxic Chemotherapy as an Immune Stimulus: A Molecular Perspective on Turning Up the Immunological Heat on Cancer

Cytotoxic chemotherapeutics (CCTs) are widely used in the treatment of cancer. Although their mechanisms of action have been best understood in terms of targeting the apparatus of mitosis, an ability to stimulate anti-tumor immune responses is increasing the recognition of these agents as immunotherapies. Immune checkpoint blockade antibodies neutralize important, but specific, immune-regulatory interactions such as PD-1/PD-L1 and CTLA-4 to improve the anti-tumor immune response. However, CCTs can provide a broad-acting immune-stimulus against cancer, promoting both T-cell priming and recruitment to the tumor, which compliments the effects of immune checkpoint blockade. A key pathway in this process is “immunogenic cell death” (ICD) which occurs as a result of tumor cell endoplasmic reticulum stress and apoptosis elicited by CCTs. ICD involves a series of non-redundant signaling events which break tolerance and license anti-tumor antigen-specific T-cells, allowing CCTs to act as “in situ” tumor vaccination tools. Not all responses are tumor cell-intrinsic, as CCTs can also modulate the broader tumor microenvironment. This modulation occurs through preferential depletion of stromal cells which suppress and neutralize robust anti-tumor immune responses, such as myeloid cell populations and Tregs, while effector CD8+ and CD4+ T-cells and NK cells are relatively spared. The immune-stimulating effects of CCTs are dependent on chemotherapy class, dose and tumor cell sensitivity to the agent, highlighting the need to understand the underlying biology of these responses. This mini review considers the immune-stimulating effects of CCTs from a molecular perspective, specifically highlighting considerations for their utilization in the context of combinations with immunotherapy.
The potential influence of breast cancer estrogen receptors’ distribution on active DNA demethylation

Alterations in DNA methylation may cause disturbances in regulation of gene expression, including drug metabolism and distribution. Moreover, many cancers, including breast cancer, are characterized by DNA hypomethylation and a decreased 5-hydroxymethylcytosine level. The abnormal cell growth found in breast carcinoma might be the result of impaired up-regulation of breast cancer receptors. Receptors’ expression in breast cancer determines clinical outcome, and it is possible that they lead to different DNA methylation patterns. Excessive steroid exposure can affect DNA methylation by promoting demethylation of CpG islands in promoter regions of genes, and hence may have an impact on promotion and progression of breast cancer cells. Tamoxifen, as a leading drug in breast cancer hormone therapy, has an ability to act like estrogen or antiestrogen depending on the type and localization of the breast cancer receptor. Further studies are needed to determine whether tamoxifen, similarly to steroids, may evoke changes in methylation pattern.
Survival Outcomes Among Patients With High-Grade Glioma Treated With 5-Aminolevulinic Acid–Guided Surgery: A Systematic Review and Meta-Analysis

Background: High-grade glioma (HGG) is associated with a dismal prognosis despite significant advances in adjuvant therapies, including chemotherapy, immunotherapy, and radiotherapy. Extent of resection continues to be the most important independent prognosticator of survival. This underlines the significance of increasing gross total resection (GTR) rates by using adjunctive intraoperative modalities to maximize resection with minimal neurological morbidity. 5-aminolevulinic acid (5-ALA) is the only US Food and Drug Administration–approved intraoperative optical agent used for fluorescence-guided surgical resection of gliomas. Despite several studies on the impact of intra-operative 5-ALA use on the extent of HGG resection, a clear picture of how such usage affects patient survival is still unavailable. Methods: A systematic review was conducted of all relevant studies assessing the GTR rate and survival outcomes [overall survival (OS) and progression-free survival (PFS)] in HGG. A meta-analysis of eligible studies was performed to assess the influence of 5-ALA-guided resection on improving GTR, OS, and PFS. GTR was defined as >95% resection. Results: Of 23 eligible studies, 19 reporting GTR rates were included in the meta-analysis. The pooled cohort had 998 patients with HGG, including 796 with newly diagnosed cases. The pooled GTR rate among patients with 5-ALA–guided resection was 76.8% (95% confidence interval, 69.1–82.9%). A comparative subgroup analysis of 5-ALA–guided vs. conventional surgery (controlling for within-study covariates) showed a 26% higher GTR rate in the 5-ALA subgroup (odds ratio, 3.8; P < 0.001). There were 11 studies eligible for survival outcome analysis, 4 of which reported PFS. The pooled mean difference in OS and PFS was 3 and 1 months, respectively, favoring 5-ALA vs. control (P < 0.001). Conclusions: This meta-analysis shows a significant increase in GTR rate with 5-ALA–guided surgical resection, with a higher weighted GTR rate (~76%) than the pivotal phase III study (~65%). Pooled analysis showed a small yet significant increase in survival measures associated with the use of 5-ALA. Despite the statistically significant results, the low level of evidence and heterogeneity across these studies make it difficult to conclusively report an independent association between 5-ALA use and survival outcomes in HGG. Additional randomized control studies are required to delineate the role of 5-ALA in survival outcomes in HGG.
Effects of elastic band resistance exercises with breathing techniques on pulmonary function in female seniors

The purpose of this study was to investigate the effects of elastic-band resistance exercises combined with breathing techniques on pulmonary function in female seniors. Forty-five female seniors 65 years or older were recruited from a welfare center and assigned to an experimental (n=23) or control (n=22) group. The experimental group used an elastic band with a resistance exercises while concurrently using specific breathing techniques. The control group conducted the same resistance tasks without the respiration exercises. Respiratory function data were collected before and after the 6-week intervention. The experimental group showed a significant increase in forced vital capacity (FVC), forced expiratory volume 1 sec (FEV1), and in FEV1 as a percentage of FVC. In addition, there were significant differences in the FVC and FEV1 levels between groups. The results show that resistance accompanied by breathing techniques positively affects senior respiratory function when an elastic band is used for exercise.
Temporal Planning as Refinement-Based Model Checking

Planning as model checking based on source-to-source compilations has found increasing attention. Previously proposed approaches for temporal and hybrid planning are based on static translations, in the sense that the resulting model checking problems are uniquely defined by the given input planning problems. As a drawback, the translations can become too large to be efficiently solvable. In this paper, we address propositional temporal planning, lifting static translations to a more flexible framework. Our framework is based on a refinement cycle that allows for adaptively computing suitable translations of increasing size. Our experiments on temporal IPC domains show that the resulting translations to timed automata often become succinct, resulting in promising performance when applied with the directed model checker MCTA.
The Clustered Dial-a-Ride Problem

We study a variant of the classical dial-a-ride problem, with an application to public transport planning in rural areas. In the classical dial-a-ride problem, n users each specify a pickup and a delivery location, and the aim is to plan the least cost route to cater all requests. This can be modeled as a traveling salesmen problem in a complete graph with precedence constraints (pick-ups need to happen before deliveries). In this paper, we consider the clustered dial-a-ride problem, where we do not operate on a complete graph but on a graph composed of serially numbered cliques where each clique is connected to the next one via a single edge. This setting is inspired by door-to-door transportation for people from remote villages who want to get to another village or the next city by a bus which operates on demand. We argue that in case the optimal route exhibits certain structural properties, it can be computed significantly faster. To make use of this observation, we devise a classification algorithm which can decide whether the optimal route exhibits these structural properties before computing it. Extensive experiments on artificial and real-world instances reveal that the majority of optimal routes indeed have the desired properties and that our classifier is an efficient tool to recognize the respective instances.