Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Differently Expressed Genes Associated With Prognosis and Growth in Colon Adenocarcinoma Based on Integrated Bioinformatics Analysis

Latest statistics showed that the morbidity and mortality of colon adenocarcinoma (COAD) ranked fourth and fifth, respectively, around the world. COAD was a heterogeneous disease, and the high rates of recurrence, metastasis, and drug resistance still posed great challenges for treatment, which needs to further develop therapeutic and prognostic targets. In this study, we got the top 3,075 differentially expressed genes (DEGs) and 1,613 potential prognostic genes by GEPIA 2 and identified 1,166 fitness genes in COAD based on genome-scale CRISPR-Cas9 knockout (GeCKO) screening data. Excluding the genes already reported in the literatures, a total of nine DEGs overlapping with prognostic and fitness genes were further analyzed. High expression of CCT6A, RHOQ, and RRP12 promoted COAD cell growth and were relative to lower survival rate of COAD patients, while high expression of UTP18, DDOST, YRDC, ACTG1, RFT1, and NLE1 also promoted COAD cell growth, but were relative to higher survival rate. In addition, CCT6A, UTP18, YRDC, RRP12, RFT1, NLE1, as well as DDOST were essential genes across pan-cancer including COAD cells, and ACTG1 and RHOQ were less essential genes in cancer cells. In a word, we discovered nine novel potential genes that could serve as anticancer targets and prognostic markers in COAD and its subtypes.
Analyzing Pedestrian Movement in Mataf Using GPS and GIS to Support Space Redesign

Evaluating the use of architectural and urban spaces is an important issue for architects and urban designers who wish to enhance space usability. Space usability is crucial in crowded spaces such as Mataf areas. Millions of people come to the city of Makkah, Saudi Arabia every year to perform Hajj (Islamic Pilgrimage) and Umrah. A cornerstone of Hajj and Umrah spirituals is to perform Tawaf, which is the circumambulation of the Ka'bah in the center of the Holy Mosque in Makkah. The areas of performing Tawaf (called Mataf) become very crowded during Hajj and the last ten days of Ramadan. This paper demonstrates how we utilized Global Positioning Systems (GPS) and Geographic Information Systems (GIS) to analyze pedestrian movement while performing Tawaf. During the Hajj of 1424 H (2004 in the Georgian Calendar), several GPS devices were used to collect pedestrian movement coordinates at specific time intervals. Computer software for tracking analysis is used to visualize and analyze the pattern of pedestrian movement in Tawaf. The software allows users to view temporal data, which can be set up with past time windows for historical data analysis. The findings of this research show levels of service and flow rates throughout different zones and times of Mataf. They indicate the most critical zones and times for Tawaf during Hajj. They also visually demonstrate the track pattern of pedestrian movement at different locations in the Tawaf area. The paper concludes with some redesign recommendations to remove obstacles and facilitate pedestrian movement in Tawaf. The approach described in this paper can be implemented in architectural and urban design space modifications to improve pedestrian movement in open spaces.
Updates on the role of imaging in the assessment of crohn's disease

As initial studies reported that magnetic resonance imaging (MRI) was useful for the evaluation of the small intestine, this modality has become increasingly important in the diagnosis, assessment and exclusion of small bowel disease. The use of MRI for the assessment of inflammatory bowel disease is increasing, at the expense of the current primary imaging modality and computed tomography (CT) enterography. MRI has many advantages over CT, including a lack of radiation exposure, lower prevalence of adverse events, availability of dynamic information, higher resolution and better soft-tissue contrast. New MRI techniques, including diffusion-weighted imaging, spectroscopy, motility study, positron-emission tomography-MRI and molecular imaging, are currently under investigation to improve the diagnosis, follow-up and management of the disease.
A Comparative Study of Pathological Outcomes in The University of Manchester Longitudinal Study of Cognition in Normal Healthy Old Age and Brains for Dementia Research Cohorts

In the present study, we have characterized and compared individuals whose brains were donated as part of The University of Manchester Longitudinal Study of Cognition in Normal Healthy Old Age (UoM) with those donated through the Manchester arm of the UK Brains for Dementia Research (BDR) program. The aim of this study was to investigate how differences in study recruitment may affect final pathological composition of cohort studies. The UoM cohort was established as a longitudinal study of aging and cognition whereas the BDR program was established, prima facie, to collect brains from both demented and non-demented individuals for the purpose of building a tissue research resource. Consequently, the differences in recruitment patterns generated differences in demographic, clinical, and neuropathological characteristics. There was a higher proportion of recruits with dementia [mostly Alzheimer’s disease (AD)] within the BDR cohort than in the UoM cohort. In pathological terms, the BDR cohort was more ‘polarized’, being more composed of demented cases with high Braak pathology scores and non-demented cases with low Braak scores, and fewer non-AD pathology cases, than the UoM cohort. In both cohorts, cerebral amyloid angiopathy tended to be greater in demented than non-demented individuals. Such observations partly reflect the recruitment of demented and non-demented individuals into the BDR cohort, and also that insufficient study time may have elapsed for disease onset and development in non-demented individuals to take place. Conversely, in the UoM cohort, where there had been nearly 30 years of study time, a broader spread of AD-type pathological changes had ‘naturally’ evolved in the brains of both demented and non-demented participants.
Genome-wide association study provides insights into the genetic architecture of bone size and mass in chickens.

Bone size is an important trait for chickens due to its association with osteoporosis in layers and meat production in broilers. Here, we employed high density genotyping platforms to detect candidate genes for bone traits. Estimates of the narrow heritabilities ranged from 0.37 ± 0.04 for shank length to 0.59 ± 0.04 for tibia length. The dominance heritability was 0.12±0.04 for shank length. Using a linear mixed model approach, we identified a promising locus within NCAPG on chromosome 4, which was associated with tibia length and mass, femur length and area and shank length. In addition, three other loci were associated with bone size or mass at a Bonferroni-corrected genome-wide significance threshold of 1%. One region on chicken chromosome 1 between 168.38 and 171.82 Mb, harboredHTR2A, LPAR6, CAB39L, and TRPC4. A second region that accounted for 2.2% of the phenotypic variance was located around WNT9A on chromosome 2, where allele substitution was predicted to be associated with tibia length. Four candidate genes identified on chromosome 27 comprising SPOP, NGFR, GIP, and HOXB3 were associated with tibia length and mass, femur length and area, and shank length. Genome partitioning analysis indicated that the variance explained by each chromosome was proportional to its length.
Vessel Detection and Tracking Method Based on Video Surveillance

Ship detection and tracking is a basic task in any vessel traffic monitored area, whether marine or inland. It has a major impact on navigational safety and thus different systems and technologies are used to determine the best possible methods of detecting and identifying sailing units. Video monitoring is present in almost all of them, but it is usually operated manually and is used as a backup system. This is because of the difficulties in implementing an efficient and universal automatic detection method that would work in quickly alternating environmental conditions for all kind of sailing units—from kayaks to seagoing merchant vessels. This paper presents a method that allows the detection and tracking of ships using the video streams of existing monitoring systems for ports and rivers. The method and the results of experiments on three sets of data using cameras with different characteristics, settings, and scene locations are presented. The experiments were carried out in variable light and weather conditions, and a wide range of unit types were used as detection objectives. The results confirm the usability of the proposed solution; however, some minor issues were encountered in the presence of ships wakes or highly unfavourable weather conditions.
Quartz Crystal Resonator Sensor With Printed-on-Crystal Coil for Dual-Harmonic Electromagnetic Contactless Interrogation

A novel quartz crystal resonator (QCR) sensor with a printed-on-crystal conductive coil, named sensor coil, is presented. The sensor coil electromagnetically coupled to an external readout coil allow to perform contactless interrogation of the QCR working as a stand-alone sensor unit. A frequency-domain readout technique is adopted that allows dual-harmonic operation by detecting the QCR frequencies of the fundamental and third harmonic, and offers first-order independence from the stand-off distance between the sensor and the readout unit. The QCR electrodes and sensor coil have been printed on a 330- ${\mu }\text{m}$ -thick bare AT-cut quartz crystal exploiting the aerosol jet printing technology. The fabricated QCR sensor has reference values of the fundamental and third harmonic frequencies at 4.77 and 14.22 MHz, respectively. Distance-independent contactless operation has been demonstrated for distances up to 12 mm. The readout frequencies deviate from reference values less than 10 and 90 ppm for the fundamental and third harmonic, respectively, thus validating the proposed principle.
Significance of BRCA2 and RB1 Co-loss in Aggressive Prostate Cancer Progression

Purpose: Previous sequencing studies revealed that alterations of genes associated with DNA damage response (DDR) are enriched in men with metastatic castration-resistant prostate cancer (mCRPC). BRCA2, a DDR and cancer susceptibility gene, is frequently deleted (homozygous and heterozygous) in men with aggressive prostate cancer. Here we show that patients with prostate cancer who have lost a copy of BRCA2 frequently lose a copy of tumor suppressor gene RB1; importantly, for the first time, we demonstrate that co-loss of both genes in early prostate cancer is sufficient to induce a distinct biology that is likely associated with worse prognosis. Experimental Design: We prospectively investigated underlying molecular mechanisms and genomic consequences of co-loss of BRCA2 and RB1 in prostate cancer. We used CRISPR-Cas9 and RNAi-based methods to eliminate these two genes in prostate cancer cell lines and subjected them to in vitro studies and transcriptomic analyses. We developed a 3-color FISH assay to detect genomic deletions of BRCA2 and RB1 in prostate cancer cells and patient-derived mCRPC organoids. Results: In human prostate cancer cell lines (LNCaP and LAPC4), loss of BRCA2 leads to the castration-resistant phenotype. Co-loss of BRCA2-RB1 in human prostate cancer cells induces an epithelial-to-mesenchymal transition, which is associated with invasiveness and a more aggressive disease phenotype. Importantly, PARP inhibitors attenuate cell growth in human mCRPC-derived organoids and human CRPC cells harboring single-copy loss of both genes. Conclusions: Our findings suggest that early identification of this aggressive form of prostate cancer offers potential for improved outcomes with early introduction of PARP inhibitor–based therapy. See related commentary by Mandigo and Knudsen, p. 1784
Multi-State Energy Classifier to Evaluate the Performance of the NILM Algorithm

With the large-scale deployment of smart meters worldwide, research in non-intrusive load monitoring (NILM) has seen a significant rise due to its dual use of real-time monitoring of end-user appliances and user-centric feedback of power consumption usage. NILM is a technique for estimating the state and the power consumption of an individual appliance in a consumer’s premise using a single point of measurement device such as a smart meter. Although there are several existing NILM techniques, there is no meaningful and accurate metric to evaluate these NILM techniques for multi-state devices such as the fridge, heat pump, etc. In this paper, we demonstrate the inadequacy of the existing metrics and propose a new metric that combines both event classification and energy estimation of an operational state to give a more realistic and accurate evaluation of the performance of the existing NILM techniques. In particular, we use unsupervised clustering techniques to identify the operational states of the device from a labeled dataset to compute a penalty threshold for predictions that are too far away from the ground truth. Our work includes experimental evaluation of the state-of-the-art NILM techniques on widely used datasets of power consumption data measured in a real-world environment.
Assistive technology: Visual mapping combined with mobile software can enhance quality of life and ability to carry out activities of daily living in individuals with impaired memory.

BACKGROUND There is growing evidence that assistive digital technology can enhance quality of life (QOL) for individuals with various forms of cognitive impairment, including dementia. OBJECTIVE Assess whether the use of a visual mapping software program to manage activities of daily living would have a positive impact on QOL scores and on cognitive scores in a group of dementia residents in an adult living community. METHODS We compared quality-of-life scores and cognitive function scores before and after using the assistive technology for three months. RESULTS 1. QOL scores significantly improved in the memory impaired residents, as measured by a self-report questionnaire. 2. Caregivers also reported significantly improved QOL scores in the residents, and the caregivers reported more improved scores than the residents did. 3. Net promoter scores for residents and caregivers showed that using visual maps was highly satisfying; they would continue using this technology. 4. Memory-impaired residents showed significantly improved scores in cognitive areas reflecting improved ability to focus and pay attention. CONCLUSIONS In addition to the positive findings in QOL and cognition, assistive technologies applied to dementia care are easy to access, easy to use, have little risk of side effects, and are relatively low in cost.
Influence of the Interactions at the Graphene–Substrate Boundary on Graphene Sensitivity to UV Irradiation

Graphene is a very promising material for electronics applications. In recent years, its sensitivity to ultraviolet (UV) irradiation has been studied extensively. However, there is no clear answer to the question, which factor has a key influence on the sensitivity of graphene to UV. In order to check the influence of the final substrate on the electrical response, graphene transferred on polymeric and non-polymeric substrate was investigated. To achieve this goal three polymeric and three non-polymeric substrates were tested. The results of the preliminary tests indicated the different character of the reaction on UV irradiation in each of group. To explain the reason of the difference, the complementary studies were done. The samples that were resistant to high temperature were annealed in a vacuum at 500 °C to get rid of water trapped between graphene and the substratum. The samples after annealing reacted less dynamically to UV irradiation. Moreover, the progress of changes in electrical response of the annealed samples had a similar character to the polymeric substrates, with the hydrophobic nature of the surface. These studies clearly prove that the sensitivity of graphene to UV irradiation is influenced by water trapped under the graphene.
Effects of a scalable home‐visiting intervention on child development in slums of urban India: evidence from a randomised controlled trial

Background An estimated 63.4 million Indian children under 5 years are at risk of poor development. Home visits that use a structured curriculum to help caregivers enhance the quality of the home stimulation environment improve developmental outcomes. However, achieving effectiveness in poor urban contexts through scalable models remains challenging. Methods Using a cluster randomised controlled trial, we evaluated a psychosocial stimulation intervention, comprising weekly home visits for 18 months, in urban slums of Cuttack, Odisha, India. The intervention is complementary to existing early childhood services in India and was run and managed through a local branch of a national NGO. The study ran from August 2013 to July 2015. We enrolled 421 children aged 10–20 months from 54 slums. Slums were randomised to intervention or control. Primary outcomes were children's cognitive, receptive language, expressive language and fine motor development assessed using the Bayley‐III. Prespecified intent‐to‐treat analysis investigated impacts and heterogeneity by gender. Trial registrations: ISRCTN89476603, AEARCTR‐0000169. Results Endline data for 378 (89.8%) children were analysed. Attrition was balanced between groups. We found improvements of 0.349 of a standard deviation (SD; p = .005, stepdown p = .017) to cognition while impacts on receptive language, expressive language and fine motor development were, respectively, 0.224 SD (p = .099, stepdown p = .184), 0.192 SD (p = .085, stepdown p = .184) and 0.111 (p = .385, stepdown p = .385). A child development factor improved by 0.301 SD (p = .032). Benefits were larger for boys. The quality of the home stimulation environment also improved. Conclusions This study shows that a potentially scalable home‐visiting intervention is effective in poor urban areas.
Structural basis for shieldin complex subunit 3–mediated recruitment of the checkpoint protein REV7 during DNA double-strand break repair

Shieldin complex subunit 3 (SHLD3) is the apical subunit of a recently-identified shieldin complex and plays a critical role in DNA double-strand break repair. To fulfill its function in DNA repair, SHLD3 interacts with the mitotic spindle assembly checkpoint protein REV7 homolog (REV7), but the details of this interaction remain obscure. Here, we present the crystal structures of REV7 in complex with SHLD3's REV7-binding domain (RBD) at 2.2–2.3 Å resolutions. The structures revealed that the ladle-shaped RBD in SHLD3 uses its N-terminal loop and C-terminal α-helix (αC-helix) in its interaction with REV7. The N-terminal loop exhibited a structure similar to those previously identified in other REV7-binding proteins, and the less-conserved αC-helix region adopted a distinct mode for binding REV7. In vitro and in vivo binding analyses revealed that the N-terminal loop and the αC-helix are both indispensable for high-affinity REV7 binding (with low-nanomolar affinity), underscoring the crucial role of SHLD3 αC-helix in protein binding. Moreover, binding kinetics analyses revealed that the REV7 “safety belt” region, which plays a role in binding other proteins, is essential for SHLD3–REV7 binding, as this region retards the dissociation of the RBD from the bound REV7. Together, the findings of our study reveal the molecular basis of the SHLD3–REV7 interaction and provide critical insights into how SHLD3 recognizes REV7.
Strength Exercise Has Different Effects on Pressure Pain Thresholds in Women with Endometriosis-Related Symptoms and Healthy Controls: A Quasi-experimental Study.

OBJECTIVE To evaluate the influence of strength exercises on remote pain sensitivity in women with endometriosis-related symptoms. DESIGN A quasi-experimental study. SETTING University Hospital, a tertiary health unit. SUBJECTS Twenty-one women with endometriosis-related symptoms and 21 healthy women provided written informed consent. METHODS The participants performed weekly exercise sessions on an extensor chair for four consecutive weeks. An electronic algometer was used to measure the pressure pain thresholds on the nondominant forearm. Heart rate and blood pressure were measured using a digital device. All measurements were taken before, immediately after, and 10 and 20 minutes after the exercise series. RESULTS Women with endometriosis-related symptoms had lower pain thresholds. Pressure pain thresholds increased immediately after exercise in healthy women, returning to baseline level 20 minutes after exercise. Women with endometriosis-related symptoms did not present significant pressure pain threshold alterations after exercise. However, they had a higher heart rate and systolic, diastolic, and average blood pressure than healthy women at all the timepoints. There were no consistent correlations between pressure pain thresholds and heart rate or blood pressure. CONCLUSIONS The strength exercise regimen used in this study increased pain thresholds in healthy women but not in women with endometriosis-related painful symptoms. The maintenance or even worsening of pain perception after exercise in women with persistent pain, such as those with endometriosis, may limit their adherence to a physical training program, which in turn could prevent them from experiencing the long-term beneficial effects of exercise.
Synthetic nucleic acid antibody prophylaxis confers rapid and durable protective immunity against Zika virus challenge

ABSTRACT Significant concerns have arisen over the past 3 y from the increased global spread of the mosquito-borne flavivirus, Zika. Accompanying this spread has been an increase in cases of the devastating birth defect microcephaly as well as of Guillain–Barré syndrome in adults in many affected countries. Currently there is no vaccine or therapy for this infection; however, we sought to develop a combination approach that provides more rapid and durable protection than traditional vaccination alone. A novel immune-based prophylaxis/therapy strategy entailing the facilitated delivery of a synthetic DNA consensus prME vaccine along with DNA-encoded anti-ZIKV envelope monoclonal antibodies (dMAb) were developed and evaluated for antiviral efficacy. This immediate and persistent protection strategy confers the ability to overcome shortcomings inherent with conventional active vaccination or passive immunotherapy. A collection of novel dMAbs were developed which were potent against ZIKV and could be expressed in serum within 24–48 h of in vivo administration. The DNA vaccine, from a previous development, was potent after adaptive immunity was developed, protecting against infection, brain and testes pathology in relevant mouse challenge models and in an NHP challenge. Delivery of potent dMAbs protected mice from the same murine viral challenge within days of delivery. Combined injection of dMAb and the DNA vaccine afforded rapid and long-lived protection in this challenge model, providing an important demonstration of the advantage of this synergistic approach to pandemic outbreaks.