Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical significance of soluble programmed cell death-1 and soluble programmed cell death-ligand 1 in patients with locally advanced rectal cancer treated with neoadjuvant chemoradiotherapy

Background Inhibition of the programmed cell death-1/programmed cell death-ligand 1 (PD-1/PD-L1) axis in combination with radiotherapy may be a promising approach to treat cancer. In the present study, we aimed to evaluate serum soluble PD-1/PD-L1 levels in patients with advanced rectal cancer treated with neoadjuvant chemoradiotherapy (CRT). Methods Serum soluble PD-L1 and PD-1 levels were measured using an enzyme-linked immunosorbent assay before and after CRT in 117 patients with low rectal cancer. Changes in the levels of sPD-L1/PD-1 after CRT, and the correlation between sPD-L1/PD-1 level and clinicopathological characteristics or disease-free survival (DFS) were evaluated. Results sPD-L1 levels significantly increased after CRT (p < 0.0001), whereas sPD-1 levels did not change significantly (p = 0.1050). High sPD-L1 before CRT was significantly associated with younger age (p = 0.044), and after CRT, with lymphovascular invasion (p = 0.021). High sPD-1 before and after CRT was significantly associated with a longer distance of the tumor from the anal verge (both p < 0.001). There was no correlation between sPD-L1 level and local PD-L1 expression on stromal immune cells. High sPD-L1 level after CRT tended to be associated with worse DFS (p = 0.0752). The multivariate analysis could not demonstrate an independent association for sPD-L1 levels after CRT with DFS. Conclusions Significant increase of sPD-L1 levels after CRT suggests that anti-PD-L1 therapy might be a potential treatment strategy in combination with CRT in advanced rectal cancer.
Deletion of suppressor of cytokine signaling 3 (SOCS3) in muscle stem cells does not alter muscle regeneration in mice after injury

Muscles of older animals are more susceptible to injury and regenerate poorly, in part due to a persistent inflammatory response. The janus kinase (Jak)/signal transducer and activator of transcription (Stat) pathway mediates inflammatory signaling and is tightly regulated by the suppressor of cytokine signaling (SOCS) proteins, especially SOCS3. SOCS3 expression is altered in the muscle of aged animals and may contribute to the persistent inflammation and impaired regeneration. To test this hypothesis, we performed myotoxic injuries on mice with a tamoxifen-inducible deletion of SOCS3 specifically within the muscle stem cell compartment. Muscle stem cell-specific SOCS3 deletion reduced muscle mass at 14 days post-injury (-14%, P < 0.01), altered the myogenic transcriptional program, and reduced myogenic fusion based on the number of centrally-located nuclei per muscle fiber. Despite the delay in myogenesis, muscles with a muscle stem cell-specific deletion of SOCS3 were still able to regenerate after a single bout or multiple bouts of myotoxic injury. A reduction in SOCS3 expression in muscle stem cells is unlikely to be responsible for the incomplete muscle repair in aged animals.
Molecular recognition and maturation of SOD1 by its evolutionarily destabilised cognate chaperone hCCS

Superoxide dismutase-1 (SOD1) maturation comprises a string of posttranslational modifications which transform the nascent peptide into a stable and active enzyme. The successive folding, metal ion binding, and disulphide acquisition steps in this pathway can be catalysed through a direct interaction with the copper chaperone for SOD1 (CCS). This process confers enzymatic activity and reduces access to noncanonical, aggregation-prone states. Here, we present the functional mechanisms of human copper chaperone for SOD1 (hCCS)–catalysed SOD1 activation based on crystal structures of reaction precursors, intermediates, and products. Molecular recognition of immature SOD1 by hCCS is driven by several interface interactions, which provide an extended surface upon which SOD1 folds. Induced-fit complexation is reliant on the structural plasticity of the immature SOD1 disulphide sub-loop, a characteristic which contributes to misfolding and aggregation in neurodegenerative disease. Complexation specifically stabilises the SOD1 disulphide sub-loop, priming it and the active site for copper transfer, while delaying disulphide formation and complex dissociation. Critically, a single destabilising amino acid substitution within the hCCS interface reduces hCCS homodimer affinity, creating a pool of hCCS available to interact with immature SOD1. hCCS substrate specificity, segregation between solvent and biological membranes, and interaction transience are direct results of this substitution. In this way, hCCS-catalysed SOD1 maturation is finessed to minimise copper wastage and reduce production of potentially toxic SOD1 species.
Evaluation of GBLUP, BayesB and elastic net for genomic prediction in Chinese Simmental beef cattle

Chinese Simmental beef cattle are the most economically important cattle breed in China. Estimated breeding values for growth, carcass, and meat quality traits are commonly used as selection criteria in animal breeding. The objective of this study was to evaluate the accuracy of alternative statistical methods for the estimation of genomic breeding values. Analyses of the accuracy of genomic best linear unbiased prediction (GBLUP), BayesB, and elastic net (EN) were performed with an Illumina BovineHD BeadChip on 1,217 animals by applying 5-fold cross-validation. Overall, the accuracies ranged from 0.17 to 0.296 for ten traits, and the heritability estimates ranged from 0.36 to 0.63. The EN (alpha = 0.001) model provided the most accurate prediction, which was also slightly higher (0.2–2%) than that of GBLUP for most traits, such as average daily weight gain (ADG) and carcass weight (CW). BayesB was less accurate for each trait than were EN (alpha = 0.001) and GBLUP. These findings indicate the importance of using an appropriate variable selection method for the genomic selection of traits and suggest the influence of the genetic architecture of the traits we analyzed.
Advancing environmental toxicology through chemical dosimetry: External exposures versus tissue residues

The tissue residue dose concept has been used, although in a limited manner, in environmental toxicology for more than 100 y. This review outlines the history of this approach and the technical background for organic chemicals and metals. Although the toxicity of both can be explained in tissue residue terms, the relationship between external exposure concentration, body and/or tissues dose surrogates, and the effective internal dose at the sites of toxic action tends to be more complex for metals. Various issues and current limitations related to research and regulatory applications are also examined. It is clear that the tissue residue approach (TRA) should be an integral component in future efforts to enhance the generation, understanding, and utility of toxicity testing data, both in the laboratory and in the field. To accomplish these goals, several key areas need to be addressed: 1) development of a risk‐based interpretive framework linking toxicology and ecology at multiple levels of biological organization and incorporating organism‐based dose metrics; 2) a broadly applicable, generally accepted classification scheme for modes/mechanisms of toxic action with explicit consideration of residue information to improve both single chemical and mixture toxicity data interpretation and regulatory risk assessment; 3) toxicity testing protocols updated to ensure collection of adequate residue information, along with toxicokinetics and toxicodynamics information, based on explicitly defined toxicological models accompanied by toxicological model validation; 4) continued development of residue‐effect databases is needed ensure their ongoing utility; and 5) regulatory guidance incorporating residue‐based testing and interpretation approaches, essential in various jurisdictions. Integr Environ Assess Manag 2011;7:7–27. © 2010 SETAC
Healthcare resource utilisation and costs of agitation in people with dementia living in care homes in England - The Managing Agitation and Raising QUality of LifE in Dementia (MARQUE) study

Background People with dementia living in care homes often experience clinically significant agitation; however, little is known about its economic impact. Objective To calculate the cost of agitation in people with dementia living in care homes. Methods We used the baseline data from 1,424 residents with dementia living in care homes (part of Managing Agitation and Raising QUality of lifE in dementia (MARQUE) study) that had Cohen-Mansfield Agitation Inventory (CMAI) scores recorded. We investigated the relationship between residents’ health and social care costs and severity of agitation based on the CMAI total score. In addition, we assessed resource utilisation and compared costs of residents with and without clinically significant symptoms of agitation using the CMAI over and above the cost of the care home. Results Agitation defined by the CMAI was a significant predictor of costs. On average, a one-point increase in the CMAI will lead to a 0.5 percentage points (cost ratio 1.005, 95%CI 1.001 to 1.010) increase in the annual costs. The excess annual cost associated with agitation per resident with dementia was £1,125.35. This suggests that, on average, agitation accounts for 44% of the annual health and social care costs of dementia in people living in care homes. Conclusion Agitation in people with dementia living in care homes contributes significantly to the overall costs increasing as the level of agitation increases. Residents with the highest level of agitation cost nearly twice as much as those with the lowest levels of agitation, suggesting that effective strategies to reduce agitation are likely to be cost-effective in this setting.
Applicability of personal laser scanning in forestry inventory

Light Detection and Ranging (LiDAR) technology has been widely used in forestry surveys in the form of airborne laser scanning (ALS), terrestrial laser scanning (TLS), and mobile laser scanning (MLS). The acquisition of important basic tree parameters (e.g., diameter at breast height and tree position) in forest inventory did not solve the problem of low measurement efficiency or weak GNSS signal under the canopy. A personal laser scanning (PLS) device combined with SLAM technology provides an effective solution for forest inventory under complex conditions with its light weight and flexible mobility. This study proposes a new method for calculating the volume of a cylinder using point cloud data obtained by a PLS device by fitting to a polygonal cylinder to calculate the diameter of the trunk. The point cloud data of tree trunks of different thickness were modeled using different fitting methods. The rate of correct tree trunk detection was 93.3% and the total deviation of the estimations of tree diameter at breast height (DBH) was -1.26 cm. The root mean square errors (RMSEs) of the estimations of the extracted DBH and the tree position were 1.58 cm and 26 cm, respectively. The survey efficiency of the personal laser scanning (PLS) device was 30m2/min for each investigator, compared with 0.91m2/min for the field survey. The test demonstrated that the PLS device combined with the SLAM algorithm provides an efficient and convenient solution for forest inventory.
Estimation of Fingertip Contact Force by Measuring Skin Deformation and Posture with Photo-reflective Sensors

A wearable device for measuring skin deformation of the fingertip---to obtain contact force when the finger touches an object---was prototyped and experimentally evaluated. The device is attached to the fingertip and uses multiple photo-reflective sensors (PRSs) to measures the distance from the PRSs to the side surface of the fingertip. The sensors do not touch the contact surface between the fingertip and the object; as a result, the contact force is obtained without changing the user's tactile sensation. In addition, the accuracy of estimated contact force was improved by determining the posture of the fingertip by measuring the distance between the fingertip and the contact surface. Based on the prototyped device, a system for estimating three-dimensional contact force on the fingertip was implemented.
2bit-TactileHand: Evaluating Tactons for On-Body Vibrotactile Displays on the Hand and Wrist

Visual interfaces can provide a great density of information. However, the required focused visual attention results in a high cognitive effort. This cognitive load significantly increases when multiple tasks are performed that also require visual attention. In this paper, we evaluate the perceptual abilities of 2bit tactons on the wrist and the hand as a type of complementary feedback. Based on our evaluation, 2bit tactons are reasonably high perceivable (≈ 92%) at the hand distributed among several fingers. Additionally, the data concluded that vibrotactile feedback on hand is significantly more accurate than the wrist, which coincides with the subjects' preference. TactileHand's feasibility was demonstrated in three pilot studies, encoding ambient, explicit and implicit information into 2bit tactons in different scenarios.
Let Your World Open: CAVE-based Visualization Methods of Public Virtual Reality towards a Shareable VR Experience

Virtual reality (VR) games are currently becoming part of the public-space entertainment (e.g., VR amusement parks). Therefore, VR games should be attractive for players, as well as for bystanders. Current VR systems are still mostly focused on enhancing the experience of the head-mounted display (HMD) users; thus, bystanders without an HMD cannot enjoy the experience together with the HMD users. We propose the "ReverseCAVE": a proof-of-concept prototype for public VR visualization using CAVE-based projection with translucent screens for bystanders toward a shareable VR experience. The screens surround the HMD user and the VR environment is projected onto the screens. This enables the bystanders to see the HMD user and the VR environment simultaneously. We designed and implemented the ReverseCAVE, and evaluated it in terms of the degree of attention, attractiveness, enjoyment, and shareability, assuming that it is used in a public space. Thus, we can make the VR world more accessible and enhance the public VR experience of the bystanders via the ReverseCAVE.
Brain Computer Interface for Neuro-rehabilitation With Deep Learning Classification and Virtual Reality Feedback

Though Motor Imagery (MI) stroke rehabilitation effectively promotes neural reorganization, current therapeutic methods are immeasurable and their repetitiveness can be demotivating. In this work, a real-time electroencephalogram (EEG) based MI-BCI (Brain Computer Interface) system with a virtual reality (VR) game as a motivational feedback has been developed for stroke rehabilitation. If the subject successfully hits one of the targets, it explodes and thus providing feedback on a successfully imagined and virtually executed movement of hands or feet. Novel classification algorithms with deep learning (DL) and convolutional neural network (CNN) architecture with a unique trial onset detection technique was used. Our classifiers performed better than the previous architectures on datasets from PhysioNet offline database. It provided fine classification in the real-time game setting using a 0.5 second 16 channel input for the CNN architectures. Ten participants reported the training to be interesting, fun and immersive. "It is a bit weird, because it feels like it would be my hands", was one of the comments from a test person. The VR system induced a slight discomfort and a moderate effort for MI activations was reported. We conclude that MI-BCI-VR systems with classifiers based on DL for real-time game applications should be considered for motivating MI stroke rehabilitation.
Previously-initiated hemodialysis as prognostic factor for in-hospital mortality in pneumonia patients with stage 5 chronic kidney disease: Retrospective database study of Japanese hospitals

Background Some clinicians keep patients in stage 5 chronic kidney disease (CKD) without hemodialysis for a while. This study investigated whether previously-initiated hemodialysis in stage 5 CKD patients may become a prognostic factor for in-hospital mortality due to pneumonia. Methods Patient data were obtained from the multi-institutional diagnosis procedure combination database between April 1, 2012 and March 31, 2016. The patients had records of pneumonia as both trigger and major diagnoses and records of end stage renal disease (ESRD) or stage 5 CKD as a comorbidity or other diagnoses on admission and aged 18 years or older. The following factors were adjusted: age, sex, body mass index, Barthel index, orientation disturbance, arterial oxygen saturation, systolic blood pressure, C-reactive protein level or the extent of consolidation on chest radiography, ambulance use, hospitalization within 90 days, and comorbidities upon admission. The primary outcome measure was all-cause in-hospital mortality obtained via multivariable logistic regression analysis using four Models. Model 1 involved complete case analysis with overlapping; one hospitalization per patient was counted as one. Model 2 involved a complete case analysis without overlapping; only the first hospitalization per patient was counted. Model 3 involved multilevel analysis clustered by hospital codes. Model 4 was created after multiple imputation for lacking adjusted factors. Results A total of 907 hospitals and 7,726 patients were identified. Hemodialysis was significantly associated with lower in-hospital mortality in all models (odds ratio [OR] = 0.68, 95% confidence interval [CI]: 0.54–0.87 in Model 1; OR = 0.71, 95% CI: 0.55–0.91 in Model 2; OR = 0.67, 95% CI: 0.52–0.86 in Model 3; and OR = 0.68, 95% CI: 0.54–0.87 in Model 4). Conclusion Previously-initiated hemodialysis may be an independent prognostic factor for in-hospital mortality in pneumonia patients with end-stage renal disease. This should be borne in mind when considering the time of initiation of dialysis.
The Effects of Navigational Orientation and User Experience on User Task Efficiency and Frustration Levels

The purpose of this research was to investigate the role of Internet and computer experience on the selection of vertical or horizontal navigation, the time to complete information-gathering tasks on the Internet, and the frustration level associated with an Internet-search task. The majority of users selected vertical navigation, but there were no statistically significant difference in time to complete tasks associated with either navigational orientation. There was a difference in time associated with experience level: subjects with more Internet and computer experience completed tasks faster. The implications for web designers debating vertical vs. horizontal navigation are discussed.
An Efficient Indexing Structure for Multidimensional Categorical Range Aggregation Query

Categorical range aggregation, which is conceptually equivalent to running a range aggregation query separately on multiple datasets, returns the query result on each dataset. The challenge is when the number of dataset is as large as hundreds or thousands, it takes a lot of computation time and I/O. In previous work, only a single dimension of the range restriction has been solved, and in practice, more applications are being used to calculate multiple range restriction statistics. We proposed MCRI-Tree, an index structure designed to solve multi-dimensional categorical range aggregation queries, which can utilize main memory to maximize the efficiency of CRA queries. Specifically, the MCRI-Tree answers any query in O(nkn-1) I/Os (where n is the number of dimensions, and k denotes the maximum number of pages covered in one dimension among all the n dimensions during a query). The practical efficiency of our technique is demonstrated with extensive experiments.
Collective Interaction Filtering Approach for Detection of Group in Diverse Crowded Scenes

Crowd behavior analysis research has revealed a central role in helping people to find safety hazards or crime optimistic forecast. Thus, it is significant in the future video surveillance systems. Recently, the growing demand for safety monitoring has changed the awareness of video surveillance studies from analysis of individuals behavior to group behavior. Group detection is the process before crowd behavior analysis, which separates scene of individuals in a crowd into respective groups by understanding their complex relations. Most existing studies on group detection are scene-specific. Crowds with various densities, structures, and occlusion of each other are the challenges for group detection in diverse crowded scenes. Therefore, we propose a group detection approach called Collective Interaction Filtering to discover people motion interaction from trajectories. This approach is able to deduce people interaction with the Expectation-Maximization algorithm. The Collective Interaction Filtering approach accurately identifies groups by clustering trajectories in crowds with various densities, structures and occlusion of each other. It also tackles grouping consistency between frames. Experiments on the CUHK Crowd Dataset demonstrate that approach used in this study achieves better than previous methods which leads to latest results.
StockSense: A Wrist-Worn Vibrotactile Display for tracking Volatile Markets

This paper presents StockSense, a prototype of a haptic wristband for tracking volatile markets. StockSense informs the user about current price changes via structured vibrotactile feedback. This system can be used for any volatile market: cryptocurrency market, stock market, etc. A preliminary study was carried out with 5 participants to investigate whether vibrotactile displays of smartphones could be integrated into the system for additional information transmission. Afterwards the system was evaluated in a study with 20 participants. The participants became familiar with the system within a short period of time and were able to recognize the displayed information on the vibrotactile display reliably. The participants rated the system as positive. Overall, the participants appreciated the functionality of the system and considered it to be suitable for this field of application.
Identification of prognostic biomarkers in colorectal cancer using a long non-coding RNA-mediated competitive endogenous RNA network

Colorectal cancer (CRC) is a highly malignant gastrointestinal tumor accompanied by poor prognosis. Long non-coding RNA (lncRNA) plays an important role in the progression and physiology of tumors as it competes with endogenous RNAs, including miRNA and mRNA. In the present study, a multi-step computational method was used to build a CRC-related functional lncRNA-mediated competitive endogenous RNA (ceRNA) network (LMCN). lncRNAs with more degrees and betweenness centrality (BC) were screened out as hub lncRNAs. Then functional enrichment analyses of lncRNAs were carried out from the Gene Ontology (GO) and Reactome pathway databases based on the ‘guilt by association’ principle. As a result, lncRNAs in the LMCN displayed specific topological characteristics in accordance with the regulatory correlation of coding mRNAs in CRC pathology. HCP5, EPB41L4A-AS1, SNHG12, and LINC00649 were screened out as hub lncRNAs which were more significantly related to the development and prognosis of CRC. The hub lncRNAs in CRC were obviously involved in functions of cell cycle arrest, vacuolar transport, histone modification, and in pathways of GPCR, signaling by Rho GTPases, axon guidance pathways, meaning that they might be potential biomarkers for diagnosis, evaluation and gene-targeted therapy of CRC. Thus, the LMCN construction method could accelerate lncRNA discovery and therapeutic development in CRC.