Miracle-dz/UniFAR-FTUs huggingface dataset:
Personalized peptide vaccination for castration-resistant prostate cancer progressing after docetaxel chemotherapy: A randomized, double-blind, placebo-controlled, phase III trial.

5033 Background: To develop a new treatment modality, we conducted a phase III randomized trial of personalized peptide vaccination (PPV) for human leukocyte antigen (HLA) -A24 positive patients with castration-resistant prostate cancer (CRPC) who failed docetaxel chemotherapy. Methods: Patients were randomly assigned in a 2:1 ratio to receive PPV or placebo. Four of 12 warehouse peptides selected based on preexisting peptide-specific immunoglobulin G levels or the corresponding placebo were subcutaneously injected 6 doses weekly followed the maximum of 30 doses bi-weekly until disease progression. The primary end point was overall survival (OS), and secondary end points were progression-free survival (PFS) and immune responses. Results: From August 2013 to April 2016, 310 patients were randomly assigned (207 to PPV and 103 to placebo), and 306 patients were analyzed by the full analysis set (204 to PPV and 102 to placebo). Baseline characteristics were balanced between groups. Estimated median OS was 16.1 months (95% CI, 13 to 18.2) with PPV and 16.9 months (95% CI, 13.1 to 20.4) with placebo (HR, 1.04; 95%CI, 0.79 to 1.37; P = 0.77). Median PFS was also not significantly different among them. Median Grade ≥ 3 adverse events were observed in 41% in both groups. The analysis of treatment arm effects among various subgroups revealed a lower HR for OS in favor of the PPV arm in patients with a < 64% neutrophil proportion (HR, 0.55; 95%CI, 0.33 to 0.93), with a significant interaction test ( P = 0.003). Conclusions: PPV did not prolong either OS or PFS in HLA-A24 positive patients with CRPC progressing after docetaxel chemotherapy. Clinical trial information: 0000113088.
Digital Versus Conventional Rehabilitation After Total Hip Arthroplasty: A Single-Center, Parallel-Group Pilot Study

Background The demand for total hip arthroplasty (THA) is rising. In the face of rapidly increasing health care costs, ensuring widespread, cost-effective rehabilitation is a priority. Technologies allowing independent home-based rehabilitation may be the key to facilitate access, improve effectiveness, and lower costs of care. Objective The aim of this study was to assess the feasibility of a novel artificial intelligence–powered digital biofeedback system following THA and compare the clinical outcomes against supervised conventional rehabilitation. Methods This was a single-center, parallel-group pilot study, with an 8-week intervention program. Patients were assessed at baseline, during the program (at 4 and 8 weeks), and 3 and 6 months after surgery. The primary outcome was the Timed Up and Go (TUG) score and secondary outcomes were the Hip dysfunction and Osteoarthritis Outcome Scale (HOOS; a patient-reported outcome) and hip range of motion (ROM). Results A total of 66 patients were included: 35 digital physiotherapy (PT) versus 31 conventional. There were no differences at baseline between groups except for lower HOOS quality of life (QoL) subscale scores in the digital PT group. Clinically relevant improvements were noted in both groups at all time points. The digital PT group showed a retention rate of 86% (30/35). Per-protocol analysis revealed a superiority of the digital PT group for all outcome measures. Intention-to-treat analysis revealed the superiority of the digital PT group at all time points for TUG (change between baseline and 4 and 8 weeks: P<.001; change between baseline and 3 and 6 months: P=.001 and P=.005, respectively), with a difference between median changes of −4.79 seconds (95% CI −7.24 to −1.71) at 6 months post-THA. Between baseline and month 6, results were also superior in the digital PT group for the HOOS sports and QoL subscales and all ROM except for standing flexion. Conclusions This study demonstrates this novel solution holds promise in rehabilitation after THA, ensuring better clinical outcomes than conventional rehabilitation while reducing dependence on human resources. Trial Registration ClinicalTrials.gov NCT03045549; https://clinicaltrials.gov/ct2/show/NCT03045549
Automatic alignment of multi-view range maps by optical stereo-tracking

Method: A low cost optical tracking system has been developed with the aim at creating an automatic procedure to align 3D point clouds captured by a structured light system. The tracking system uses stereo images and retro-reflective infrared markers rigidly connected to the scanner. Markers are accurately tracked on the basis of automatic intensity-based analyses. Stereo correspondences are established by using epipolar and similarity constraints.
Skin Acute Wound Healing: A Comprehensive Review

Experimental work of the last two decades has revealed the general steps of the wound healing process. This complex network has been organized in three sequential and overlapping steps. The first step of the inflammatory phase is an immediate response to injury; primary sensory neurons sense injury and send danger signals to the brain, to stop bleeding and start inflammation. The following target of the inflammatory phase, led by the peripheral blood mononuclear cells, is to eliminate the pathogens and clean the wound. Once this is completed, the inflammatory phase is resolved and homeostasis is restored. The aim of the proliferative phase, the second phase, is to repair wound damage and begin tissue remodeling. Fibroplasia, reepithelialization, angiogenesis, and peripheral nerve repair are the central actions of this phase. Lastly, the objective of the final phase is to complete tissue remodeling and restore skin integrity. This review provides present day information regarding the status of the participant cells, extracellular matrix, cytokines, chemokines, and growth factors, as well as their interactions with the microenvironment during the wound healing process.
Architecture and the four encounters with complexity

Abstract In the surge of scientific revelations concerning chaos, cybernetics and systems theory since the Second World War, architecture has been drawn into several encounters with dynamic complexity. Architects have often danced with this complexity, but there has never been a full embrace—the encounters only amounting to skirmishes between two radically different perspectives. Increasingly however, these two histories of design and science are convergent, drawn together by forces of post-industrial knowledge, society, globalization, economic interdependence and ecological sustenance. Through past literature, that convergence can be framed by four modes of architectural complexity—wicked, messy, ordered and natural—but the history of these encounters has seldom been couched in terms of their teleological and dynamic influences, nor have their separate operations been characterized or connected in a way that adds coherence. This paper addresses this missing history by making explicit distinctions between each of the four modes of architectural complexity, tracing their early proponents and characterizing their operations.
Posture, muscle endurance and ROM in individuals with and without neck pain

Abstract Introduction: Factors such as postural changes, reduced neck muscle endurance and reduced range of motion (ROM) are common characteristics attributed to people with neck pain. Objective: (a) Identify differences in postural, muscular endurance and ROM characteristics between individuals with and without neck pain and (b) relate the presence and intensity of neck pain with the characteristics of static posture, muscular endurance and cervical ROM. Method: A cross-sectional study with 60 subjects equally divided into two groups with respect to the presence of neck pain carrying out the following evaluations: (1) static postural evaluation by digital photogrammetry; (2) the neck flexor endurance test; and (3) evaluation of cervical ROM using a fleximeter. The data were analyzed with independent t-tests, the Mann-Whitney U test, and the Spearman and Tau of Kendall correlation tests (α < 0.05). Results: There were no statistical differences between individuals with and without neck pain regarding the postural, muscle endurance and cervical ROM characteristics. No statistically significant correlations were found between pain and posture, muscle endurance and cervical ROM. Conclusion: Individuals with neck pain do not appear to present differences in their postural, neck flexor muscle endurance or cervical ROM characteristics when compared to individuals without neck pain, and neck pain appears to be unrelated to these variables.
Assessing molecular subtypes of gastric cancer: microsatellite unstable and Epstein-Barr virus subtypes. Methods for detection and clinical and pathological implications

Background The molecular classification of gastric cancer recognises two subtypes prone to immune checkpoint blockade: the microsatellite unstable and the Epstein-Barr virus (EBV)-related tumours. We aim to assess the concordance between immunohistochemistry and PCR for microsatellite status evaluation, and explore the value of microsatellite instability (MSI) and EBV as predictive survival factors. Material and methods We collected 246 consecutively diagnosed gastric cancer cases in all stages and evaluated the microsatellite status using immunohistochemistry for mismatched repair (MMR) proteins and PCR. EBV expression was studied through in situ hybridisation. Results Forty-five (18%) cases presented MSI and 13 (6%) were positive for EBV. MSI was associated with female sex, older age, distal location and distal non-diffuse type of the modified Lauren classification. EBV expression was most frequent in proximal location and proximal non-diffuse type. The sensitivity, specificity, positive predictive value and negative predictive value of immunohistochemistry for the microsatellite study were 91%, 98%, 91% and 98%, respectively. In the multivariate analysis, MSI was an independent predictor of favourable tumour-specific survival (TSS) in stages I–III (MSI: HR: 0.37, 95% CI 0.12 to 0.95, p=0.04). Conclusions The MSI status and the EBV expression should be incorporated in routine pathological report for two reasons. First, MSI defines a different pathological entity with a better outcome. Second, MSI and EBV may be useful biomarkers to identify patients who will respond to immune checkpoint blockade inhibitors. For this purpose, immunohistochemical study for MMR proteins and in situ hybridisation study for EBV evaluation are feasible and cost-effective methods.
Applied positioning method for hand-eye vision system

In this paper,the hand-eye problem is reformulated and a new system model is obtained,by which an effective system calibration method is presented.The key is directly mapping the camera coordinate to the robot coordinate,and the system parameters can be obtained as a whole without considering every one therein.Compared with the original method,there is not any restriction to the system positioning,that is to say,the camera can take images at any pose and the system needn't to be recalibrated.Experiments show that this algorithm is quick and convenient to be applied;the experimental procedure is simple and positioning results are precise.This method overcomes the limitation of the original one and extends the application range of hand-eye vision system.
The effect of endurance training on body composition and blood lipids in older adults : a randomized controlled trial

4 Table of contents . 5 1.0 INTRODUCTION . 7 1.1 Age-related changes in body composition . 7 1.2 Age-related changes in lipid profile . 8 1.3 Endurance training and elderly . 9 1.4 The present study . 10 2.0 METHODS . 10 2.1 Study design . 10 2.2 Participants . 11 2.3 Equipment and materials . 11 2.3.1 Body composition analyzer . 11 2.3. 2 Blood lipids . 12 2.3. 3 Anthropometry . 13 2.4 Procedure . 13 2.4. 1 Body composition . 13 2.4. 2 Anthropometry . 14 2.4. 2.1 Height . 14 2.4. 2.2 Waist circumference . 14 2.4. 3 Blood lipids . 14 2.5 Intervention . 15 2.5. 1 Moderate-intensity training . 15 2.5. 2 High-intensity training . 15 2.5. 3 Control group . 16 2.6 Adherence . 16 2.7 Statistical analyses . 16 3.0 RESULTS . 16 3.1 Sample characteristics . 17
Finding Syntactic Structure in Unparsed Corpora

The Gsearch system allows the selection of sentences by syntactic criteria from text corpora, even when these corpora contain no prior syntactic markup. This is achieved by means of a fast chart parser, which takes as input a grammar and a search expression specified by the user. Gsearch features a modular architecture that can be extended straightforwardly to give access to new corpora. The Gsearch architecture also allows interfacing with external linguistic resources (such as taggers and lexical databases). Gsearch can be used with graphical tools for visualizing the results of a query.
A method for examining metadata quality in open research datasets using the OAI-PMH and SQL queries: the case of the Dublin Core 'Subject' element and suggestions for user-centred metadata annotation design

Poor quality metadata can have negative impact not only on the way research datasets are retrieved, shared and used by scientists, but also on the way research data repositories are managed and audited. The aim of the research reported in this paper was to perform a descriptive analysis of the Dublin Core's Subject metadata element and identify its quality problems, if any, in the context of the Dryad research data repository following a novel data-preprocessing method using SQL queries. The findings showed quality problems related to the lack of controlled vocabulary and standardisation, like the inconsistent use of singular and plural forms, adjectives and synonyms. This study has both practical and methodological implications for the evaluation of metadata and the improvement of the quality of the research data annotation process in open research data repositories.
High-level ciprofloxacin resistance among hospital-adapted (CC17)

Hospital-adapted differ from their colonising variants in humans and animals by additional genomic content. Molecular typing based on multilocus sequence typing (MLST) allows allocation of isolates to specific clonal complexes (CCs), such as CC17 for hospital-adapted strains. Acquired ampicillin resistance is a specific feature of these hospital isolates, especially in Europe. A few recent reports have described acquired high-level ciprofloxacin resistance as a supposed feature of hospital-adapted strains. In the present retrospective analysis, ciprofloxacin minimum inhibitory concentrations (MICs) of 609 clinical isolates from German hospital patients (1997–2007) were determined and a breakpoint for high-level resistance was deduced (>16mg/L). Acquired high-level ciprofloxacin resistance was distributed among isolates of 26 different MLST types (all CC17), indicating a wide prevalence of this acquired resistance trait among the hospital-adapted population. High-level ciprofloxacin resistance was linked to and mutations in 98 investigated isolates. Eleven different allele types or combinations thereof were identified. Their allocation to specific MLST and pulsed-field gel electrophoresis (PFGE) types revealed differences in the emergence and spread of corresponding mutations and strains.
Somatic genetic aberrations in gallbladder cancer: comparison between Chinese and US patients.

Background Gallbladder cancer (GBC) is often diagnosed at an advanced stage with limited therapeutic options and poor prognosis. The five-year survival rate of this cancer when diagnosed at an advanced stage is below 5%, and the median survival time is less than a year with standard gemcitabine-based chemotherapy. Survival benefit with second-line treatment is unknown. Thus, there is an urgent need for novel treatment strategies and targeted therapy based on next generation sequencing (NGS) may be of value. Methods Comprehensive genomic profiling (CGP) was performed with NGS panel on paraffin-embedded tumors from a cohort of 108 Chinese and 107 US GBC patients. Clinical data were collected using an IRB approved protocol from a single-center in US and from China. Results In Chinese and US GBC cohorts, an average of 6.4 vs. 3.8 genomic alterations (GAs) were identified per patient. The most frequent alterations were TP53 (69.4%), CDKN2A/B (26%), ERBB2 (18.5%), PIK3CA (17%) and CCNE1 (13%) in Chinese cohort, TP53 (57.9%), CDKN2A/B (25%), SMAD4 (17%), ARID1A (14%), PIK3CA (14%) and ERBB2 (13.1%) in US patients. NFE2L2 mutations were present in 6.5% of Chinese patients and not observed in the US cohort. Interestingly, ERBB2 genetic aberrations were significantly associated with better pathological tumor differentiation and tended to co-occurrence with CDKN2A/B mutations in both the Chinese and US GBC cases. Out of the top 9 dysregulated genetic pathways in cancer, Chinese patients harbored more frequent mutations in ERBB genes (30.6% vs. 19.0%, P=0.04). High frequency of PI3K/mTOR pathway variations was observed in both Chinese (37%) and US cohort (33%) (P=0.5). Additionally, both Chinese and US GBC patients exhibited a relatively high tumor mutational burden (TMB) (17.6% and 17.0%, respectively). In the Chinese cohort, a significant association was seen between direct repair gene alterations and TMB ≥10 muts/Mb (P=0.004). Conclusions In our study, over 83% Chinese and 68% US GBC patients had actionable alterations that could potentially guide and influence personalized treatment options. The identification of high TMB, ERBB2, CDKN2A/B, PI3K/mTOR pathway and DNA repair mutations indicated that both Chinese and US GBC patients may benefit from targeted or immune checkpoint inhibitors.
Early real-world effectiveness of ustekinumab for Crohn’s disease

Objective To understand the effectiveness of ustekinumab in treating Crohn’s disease (CD) in a UK real-world setting. Design Retrospective cohort study using prospectively maintained clinical records. Setting Single UK inflammatory bowel disease centre. Patients Adult patients with an established diagnosis of CD prescribed ustekinumab outside of clinical trials at University Hospital Southampton (UHS). Interventions Ustekinumab, a monoclonal antibody to the shared p40 subunit of interleukin (IL) 12 and IL-23 as part of routine clinical care. Main outcome measures Effectiveness as measured by an improvement in physician’s global assessment, drug persistence and improvement in biomarkers (C-reactive protein (CRP), albumin and calprotectin). Results 84 patients were included, 72 had a postinduction review and 49 had 1-year data. At postinduction clinical review, clinical response occurred in 53% of patients and clinical remission occurred in 8%. For patients on ustekinumab at 1 year, clinical response occurred in 71% and remission in 14%. Adverse events included four patients with infections requiring admission, one drug-related rash, five CD surgeries and two CD exacerbations. Conclusions Ustekinumab was well tolerated in a complex UK CD population and demonstrated benefit to patients in terms of clinical response and improvement of biomarkers and with some patients attaining clinical remission. No unexpected safety signals were seen.
An alternative approach to reduce algorithm‐derived biases in monitoring soil organic carbon changes

Abstract Quantifying soil organic carbon (SOC) changes is a fundamental issue in ecology and sustainable agriculture. However, the algorithm‐derived biases in comparing SOC status have not been fully addressed. Although the methods based on equivalent soil mass (ESM) and mineral‐matter mass (EMMM) reduced biases of the conventional methods based on equivalent soil volume (ESV), they face challenges in ensuring both data comparability and accuracy of SOC estimation due to unequal basis for comparison and using unconserved reference systems. We introduce the basal mineral‐matter reference systems (soils at time zero with natural porosity but no organic matter) and develop an approach based on equivalent mineral‐matter volume (EMMV). To show the temporal bias, SOC change rates were recalculated with the ESV method and modified methods that referenced to soils at time t1 (ESM, EMMM, and EMMV‐t1) or referenced to soils at time zero (EMMV‐t0) using two datasets with contrasting SOC status. To show the spatial bias, the ESV‐ and EMMV‐t0‐derived SOC stocks were compared using datasets from six sites across biomes. We found that, in the relatively C‐rich forests, SOC accumulation rates derived from the modified methods that referenced to t1 soils and from the EMMV‐t0 method were 5.7%–13.6% and 20.6% higher than that calculated by the ESV method, respectively. Nevertheless, in the C‐poor lands, no significant algorithmic biases of SOC estimation were observed. Finally, both the SOC stock discrepancies (ESV vs. EMMV‐t0) and the proportions of this unaccounted SOC were large and site‐dependent. These results suggest that although the modified methods that referenced to t1 soils could reduce the biases derived from soil volume changes, they may not properly quantify SOC changes due to using unconserved reference systems. The EMMV‐t0 method provides an approach to address the two problems and is potentially useful since it enables SOC comparability and integrating SOC datasets.
Low expression of miR-125a-5p is associated with poor prognosis in patients with gastric cancer

microRNAs (miRs) serve critical roles in tumor progression. Low expression of miR-125a in gastric carcinoma (GC) may promote tumor development. In the present study, low expression of miR-125a was confirmed in cancer tissues using The Cancer Genome Atlas database. Additionally, the expression and clinical significance of miR-125a-5p was investigated using reverse transcription-quantitative PCR in 150 cases of GC. The results of the present study demonstrated that the level of miR-125a-5p expression was decreased in GC biopsies compared with that in matched adjacent normal tissues. Low expression of miR-125a-5p was associated with increased tumor diameter, high Ki67 expression and poor overall survival of patients with GC. Multivariate survival analysis demonstrated that low miR-125a-5p expression may be used as an independent prognostic factor for patients with GC. However, no effects on the cell viability in a Cell Counting kit-8 assay, and cell migration and invasion in Transwell assays were detected in response to treatment using miR-125a-5p mimics or inhibitors in vitro. Therefore, the results of the present study provide evidence that low expression of miR-125a-5p may be associated with a poor prognosis, suggesting its value as a tumor biomarker for patients with GC.