Miracle-dz/UniFAR-FTUs huggingface dataset:
Low expression of VSIG4 is associated with poor prognosis in hepatocellular carcinoma patients with hepatitis B infection

Background V-set and immunoglobulin domain containing protein 4 (VSIG4) was reported to play an important role in tumorigenesis. However, the expression and clinical relevance in hepatocellular carcinoma (HCC) remain unknown. Materials and methods First, the mRNA profiles of HCC were screened from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases. VSIG4, a differentially expressed gene that has not been reported in HCC, was distinguished. Second, the correlation between VSIG4 expression and the prognosis of HCC patients from TCGA was analyzed. Third, VSIG4 mRNA level was detected in 36 pairs of HCC tissues and 4 HCC cell lines by PCR assay. And finally, prognosis analysis was assessed for 36 HCC patients with different expression levels of VSIG4. Results Bioinformatics analysis showed that VSIG4 expression was downregulated in HCC tissues, and the expression level of VSIG4 was negatively correlated with serum alpha fetal protein (AFP) level and tumor distant metastasis. Survival analysis of all HCC patients in TCGA indicated that the overall survival and disease-free survival were not significantly associated with VSIG4 expression. However, subgroup analysis showed that in the patients with hepatitis B virus-related HCC, both overall survival and disease-free survival were shorter in the low VSIG4 expression group. Our PCR results further showed that VSIG4 expression was significantly decreased in HCC tissues and HCC cell lines, and the disease-free survival in hepatitis B virus-related HCC patients with low VSIG4 expression was shorter than in those with high VSIG4 expression, which was consistent with the bioinformatics analysis results. Conclusion Our study suggests that VSIG4 is downregulated in HCC, and low expression of VSIG4 is associated with poor prognosis in hepatitis B virus-related HCC patients.
Sensory Modulation: An Important Piece of the Disability Puzzle for Adolescents With Persistent Pain

Objectives: Sensory modulation patterns contribute to altered pain perception and disengagement in activities; atypical sensory modulation patterns have been associated with higher pain sensitivity, catastrophizing, and reduced function. Objectives of this study were to ascertain whether: adolescents with persistent pain had atypical sensory modulation patterns, atypical sensory modulation was associated with reduced functioning and higher pain, and pain catastrophizing mediated the relationship between sensory modulation and functional disability. Methods: Adolescents (N=70, females=63, males=7) attending tertiary level interdisciplinary team assessment for persistent pain completed sensory modulation (Adolescent/Adult Sensory Profile), pain catastrophizing (Bath Adolescent Pain Questionnaire), pain intensity, functional disability (Functional Disability Index), and quality of life (QOL) (Pediatric QOL Scales) questionnaires. Results: Adolescents with persistent pain had atypical patterns of sensory modulation compared with normative data. Sensory modulation patterns were not associated with pain intensity; however, higher sensitivity was associated with greater disability (r=0.36, P<0.01), and lower registration of sensation was associated with poorer emotional (r=0.31, P<0.01), social (r=0.35, P<0.01), and school-related (r=0.49, P<0.001) QOL. Sensory modulation, pain intensity, and catastrophizing contributed independently to disability; catastrophizing mediated sensory sensitivity and both functional disability and emotional QOL. Discussion: This study is the first to show that atypical sensory modulation patterns are associated with poorer function for adolescents with persistent pain, suggesting that individualized sensory-informed interventions can potentially facilitate participation in daily activities and improve QOL.
Stereotactic radiosurgery for vestibular schwannomas

Stereotactic radiosurgery (SRS) maintains an important role in managing vestibular schwannoma (VS). Long-term clinical data have clearly established the safety and efficacy of the procedure for managing Koos low grade to intermediate grade VS. Historically, the procedure was developed via a multidisciplinary approach that involves physicians (eg, neurosurgeons and radiation oncologists) as well as clinical specialists (eg, radiation physicists). In this paper, we have reviewed current technical and clinical practices of SRS for VS from a procedural specialist’s perspective and from a clinician’s perspective.
Lived experience of a child’s chronic illness and death: A qualitative systematic review of the parental bereavement trajectory

Abstract To understand the lived experience of parents who have lost their child to a chronic life-limiting condition, six major databases were searched by adhering to the Preferred Reporting Items for Systematic Review and Meta-Analyses guidelines. Articles were screened for appropriateness using the Sample, Phenomenon of Interest, Design, Evaluation, Research type tool, and relevant qualitative studies were selected for full-text data analysis using Thematic Synthesis. Findings were categorized into 13 themes that were further organized into a four-phase trajectory of parental bereavement experience of child loss, namely: Liminal Margin, Holding Space, Navigating Losses, and Reconstructing Lives. The findings are discussed in the light of existing literature with practical recommendations for enhancing parental bereavement support services.
Trunk control and gross motor outcomes after body weight supported treadmill training in young children with severe cerebral palsy: a non-experimental case series

ABSTRACT Objective: To explore the impact of a body weight supported treadmill training (BWSTT) intervention on postural control and gross motor function in three young children with cerebral palsy (CP) classified as Gross Motor Function Classification System (GMFCS) levels IV or V. Method: Children (N = 3) between the ages of 2–3 years who were diagnosed with CP classified as GMFCS levels IV and V participated in BWSTT three times per week. The Segmental Assessment of Trunk Control (SATCo) and the gross motor function measure (GMFM-66) were assessed before and after the 6-week intervention. Results: Final testing revealed that all participants improved on the SATCo and GMFM. Conclusion: BWSTT is a viable intervention that may improve trunk control and gross motor outcomes in young children with severe CP. Further research is needed to explore the impact of BWSTT for young children classified as GMFCS levels IV and V.
Generalized Inverse Optimization through Online Learning

Inverse optimization is a powerful paradigm for learning preferences and restrictions that explain the behavior of a decision maker, based on a set of external signal and the corresponding decision pairs. However, most inverse optimization algorithms are designed specifically in batch setting, where all the data is available in advance. As a consequence, there has been rare use of these methods in an online setting suitable for real-time applications. In this paper, we propose a general framework for inverse optimization through online learning. Specifically, we develop an online learning algorithm that uses an implicit update rule which can handle noisy data. Moreover, under additional regularity assumptions in terms of the data and the model, we prove that our algorithm converges at a rate of $\mathcal{O}(1/\sqrt{T})$ and is statistically consistent. In our experiments, we show the online learning approach can learn the parameters with great accuracy and is very robust to noises, and achieves a dramatic improvement in computational efficacy over the batch learning approach.
Colorectal cancer combination therapy using drug and gene co-delivered, targeted poly(ethylene glycol)-ε-poly(caprolactone) nanocarriers

Purpose Combination therapy is a promising strategy to treat cancer due to the synergistic effects. The drug and gene co-delivered systems attract more attention in the field of combination therapy. Materials and methods In the present research, poly(ethylene glycol)-ε-poly(caprolactone) block copolymer was used for the co-loading of 5-fluorouracil (5-FU) and gene. The physicochemical characteristics, in vitro and in vivo anticancer, and gene transfection efficiency were tested on colon cancer cells and tumor-bearing mice. Results 5-FU and gene co-loaded nanocarriers had a size of 145 nm. In vivo gene delivery results showed about 60% of gene-positive cells. Tumor volume of nanocarrier groups at day 21 was around 320 mm3, which is significantly smaller compared with free 5-FU group (852 mm3) and control group (1,059 mm3). The maximum 5-FU plasma concentration in nanocarrier groups (49 µg/mL) was significantly greater than free 5-FU (13 µg/mL). At 24 hours, drug level of nanocarrier groups was about 2.8 µg/mL compared with 0.02 µg/mL of free 5-FU. Conclusion The resulting nanocarriers co-loaded with the anticancer drugs and genes could be considered as a promising nanomedicine for colorectal cancer therapy.
Considerations for Measurement of Embryonic Organ Growth

Organogenesis is a complex coordinated process of cell proliferation, growth, migration, and apoptosis. Differential growth rates, particularly during cardiogenesis, play a role in establishing morphology. Studies using stereological and cell sorting methods derive averages of morphogenetic parameters for an organ. To understand tissue composition and differential growth, the researcher must determine a number of morphogenetic parameters in the developing organ. Such measurements require sectioning to enable identification of organ borders, tissue components and cell types, three‐dimensional (3D)‐reconstruction of sections to visualize morphology and a 3D‐measurement scheme to build local morphogenetic information. Although thick the section confocal microscopy partially solves these issues, information loss at the section surface hampers the reconstruction of 3D morphology. Episcopic imaging provides the correct morphology but lacks histological procedures to identify multiple cell types. The 3D‐measurement scheme is based on systematic sampling, with overlapping sample volumes, of the entire organ in the aligned image stack. For each sample volume, morphogenetic variables are calculated and results projected back to the cube (boxel) at the sample volume center. Boxel size determines spatial resolution of the final quantitative 3D‐reconstruction whereas size of the sample volume determines the precision of the morphogenetic information. The methods described here can be used to measure tissue volume, proliferation and cell size, to determine contribution and distribution of cell types in a tissue and to display this information in a quantitative 3D‐reconstruction. Anat Rec, 302:49‐57, 2019. © 2018 The Authors. The Anatomical Record published by Wiley Periodicals, Inc. on behalf of American Association of Anatomists
Contextual Multi-Armed Bandits for Causal Marketing

This work explores the idea of a causal contextual multi-armed bandit approach to automated marketing, where we estimate and optimize the causal (incremental) effects. Focusing on causal effect leads to better return on investment (ROI) by targeting only the persuadable customers who wouldn't have taken the action organically. Our approach draws on strengths of causal inference, uplift modeling, and multi-armed bandits. It optimizes on causal treatment effects rather than pure outcome, and incorporates counterfactual generation within data collection. Following uplift modeling results, we optimize over the incremental business metric. Multi-armed bandit methods allow us to scale to multiple treatments and to perform off-policy policy evaluation on logged data. The Thompson sampling strategy in particular enables exploration of treatments on similar customer contexts and materialization of counterfactual outcomes. Preliminary offline experiments on a retail Fashion marketing dataset show merits of our proposal.
Characteristics, behaviours and readiness of persons seeking hearing healthcare online

Abstract Objective: This study describes characteristics, behaviours and readiness of people who are interested in seeking hearing healthcare (HHC) online. Design: A non-profit clinic was established from which services through a virtual clinic are offered. Most of the patient–audiologist interactions are conducted online. We used online means to invite individuals to take a free online digit-in-noise (DIN) test. Upon failing the test, individuals reported their readiness to seek HHC by using two tools: the line and the staging algorithm. Study sample: Individuals ≥18 years of age, within the greater Durban area, South Africa, were eligible to participate in the study. Results: A total of 462 individuals completed the online DIN test during the first 3 months. Of those, 58.66% (271/462) failed the test and 11.04% (51/462) submitted their details for further contact from the clinic audiologist. Five individuals proceeded to a comprehensive hearing evaluation and hearing aid trial: all those individuals showed readiness to seek further HHC on the measurement tools. These individuals have reported knowing of their hearing challenges prior to taking the test and have waited for a period of between 5 and 16 years before seeking HHC. A significant association between age and DIN test result was found. Conclusion: This explorative study is the first clinic to utilise digital tools across the entire patient journey in combination with face-to-face interactions in providing HHC. Internet-connected devices provide an opportunity for individuals to seek HHC and for providers to offer initial services to detect, counsel and support persons through the initial engagement process of seeking HHC. This may open up new audiology patient pathways through online hearing screening, assessment of readiness to seek further HHC and enhancement of service delivery using hybrid services by combining online and face-to-face modes of synchronous and asynchronous communication.
VSTM2A Overexpression Is a Sensitive and Specific Biomarker for Mucinous Tubular and Spindle Cell Carcinoma (MTSCC) of the Kidney

Our recent study revealed recurrent chromosomal losses and somatic mutations of genes in the Hippo pathway in mucinous tubular and spindle cell carcinoma (MTSCC). Here, we performed an integrative analysis of 907 renal cell carcinoma (RCC) samples (combined from The Cancer Genome Atlas and in-house studies) and the Knepper data set of microdissected rat nephrons. We identified VSTM2A and IRX5 as novel cancer-specific and lineage-specific biomarkers in MTSCC. We then assessed their expression by RNA in situ hybridization (ISH) in 113 tumors, including 33 MTSCC, 40 type 1 papillary RCC, 8 type 2 papillary RCC, 2 unclassified RCC, 15 clear cell RCC, and 15 chromophobe RCC. Sensitivity and specificity were calculated as the area under the receiver operating characteristics curve (AUC). All MTSCC tumors demonstrated moderate to high expression of VSTM2A (mean ISH score=255). VSTM2A gene expression assessed by RNA sequencing strongly correlated with VSTM2A ISH score (r2=0.81, P=0.00016). The majority of non-MTSCC tumors demonstrated negative or low expression of VSTM2A. IRX5, nominated as a lineage-specific biomarker, showed moderate to high expression in MTSCC tumors (mean ISH score=140). IRX5 gene expression assessed by RNA sequencing strongly correlated with IRX5 ISH score (r2=0.69, P=0.00291). VSTM2A (AUC: 99.2%) demonstrated better diagnostic efficacy than IRX5 (AUC: 87.5%), and may thus serve as a potential diagnostic marker to distinguish tumors with overlapping histology. Furthermore, our results suggest MTSCC displays an overlapping phenotypic expression pattern with the loop of Henle region of normal nephrons.
Bacterial Associates of a Gregarious Riparian Beetle With Explosive Defensive Chemistry

Bombardier beetles (Carabidae: Brachininae) are well known for their unique explosive defensive chemistry. These beetles are found in riparian corridors throughout the American Southwest, where they commonly form large diurnal multispecies aggregations in moist areas under rocks, in crevices, and in leaf litter. Using high throughput 16S amplicon sequencing, we provide the first microbiome survey of a bombardier beetle, Brachinus elongatulus, collected from two sites in Arizona. Two bacterial taxa were present in all individuals sampled: Enterococcus and Dysgonomonas. Enterococcus has been implicated in the production of fecal aggregation pheromone components, which have been shown to regulate aggregation in the German cockroach; it is possible that Enterococcus plays a similar role in Brachinus. Dysgonomonas was found in all the secretory cells of the defensive system and gut samples. Additional studies are needed to determine if these microbes play a role in these beetles’ unique chemical defense. Results also show that the majority of B. elongatulus individuals collected from both sites were infected with Spiroplasma. Many Spiroplasma are intracellular, vertically transmitted insect symbionts that may manipulate host reproduction (e.g., cause male-killing) or provide resistance to nematodes and/or parasitoid wasps. Defensive protection could be especially beneficial to B. elongatulus, which are frequently parasitized by horsehair worms (Nematomorpha). In sum, findings suggest several testable hypotheses on the effects bacteria may have on bombardier beetle behavior and physiology.
Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation

Abstract DNA damage can affect various regulatory elements of the genome, with the consequences for DNA structure, dynamics, and interaction with proteins remaining largely unexplored. We used solution NMR spectroscopy, restrained and free molecular dynamics to obtain the structures and investigate dominant motions for a set of DNA duplexes containing CpG sites permuted with combinations of 5-methylcytosine (mC), the primary epigenetic base, and 8-oxoguanine (oxoG), an abundant DNA lesion. Guanine oxidation significantly changed the motion in both hemimethylated and fully methylated DNA, increased base pair breathing, induced BI→BII transition in the backbone 3′ to the oxoG and reduced the variability of shift and tilt helical parameters. UV melting experiments corroborated the NMR and molecular dynamics results, showing significant destabilization of all methylated contexts by oxoG. Notably, some dynamic and thermodynamic effects were not additive in the fully methylated oxidized CpG, indicating that the introduced modifications interact with each other. Finally, we show that the presence of oxoG biases the recognition of methylated CpG dinucleotides by ROS1, a plant enzyme involved in epigenetic DNA demethylation, in favor of the oxidized DNA strand. Thus, the conformational and dynamic effects of spurious DNA oxidation in the regulatory CpG dinucleotide can have far-reaching biological consequences.
Making Sense of Risk—A Sociological Perspective on the Management of Risk

This article describes how risk has been conceptualized in the business and organizational literature through four distinct transformations: from the techno‐scientific perspective to the cognitive, the social‐cultural, and, finally, to the constructionist perspective. Each domain conceptualizes risk in different ways, as organizations have found it difficult to understand and mitigate using the risk management tools available. Conceptualizing risk as sensemaking becomes relevant due to the complexity of information available to the risk manager, and, coupled with time constraints, this means that risk managers increasingly rely on making sense of possible threats rather than on the accuracy of the information received. This shift presents four contributions to the current literature. First, it suggests that the role of risk management is shifting from being technical in nature to being about risk sensemaking, where the manager engages with the social and physical environment with the aim of acquiring cues that could indicate how future events will unfold. Second, a sensemaking perspective implies a shift in the use of risk management systems from being “containers” of knowledge about past risk events to lending legitimacy to the plausibility of the success of future decisions. Third, the role of the risk manager in managing individual risks changes and becomes one of managing everything using the social networks and systems available as indicators of future risk events. Finally, the risk manager and the systems he or she relies upon are regarded as a source of risk in themselves as both act as gatekeepers for organizational risk decision making.
Semi-Supervised Methods for Out-of-Domain Dependency Parsing

Dependency parsing is one of the important natural language processing tasks that assigns syntactic trees to texts. Due to the wider availability of dependency corpora and improved parsing and machine learning techniques, parsing accuracies of supervised learning-based systems have been significantly improved. However, due to the nature of supervised learning, those parsing systems highly rely on the manually annotated training corpora. They work reasonably good on the in-domain data but the performance drops significantly when tested on out-of-domain texts. To bridge the performance gap between in-domain and out-of-domain, this thesis investigates three semi-supervised techniques for out-of-domain dependency parsing, namely co-training, self-training and dependency language models. Our approaches use easily obtainable unlabelled data to improve out-of-domain parsing accuracies without the need of expensive corpora annotation. The evaluations on several English domains and multi-lingual data show quite good improvements on parsing accuracy. Overall this work conducted a survey of semi-supervised methods for out-of-domain dependency parsing, where I extended and compared a number of important semi-supervised methods in a unified framework. The comparison between those techniques shows that self-training works equally well as co-training on out-of-domain parsing, while dependency language models can improve both in- and out-of-domain accuracies.
The proof is in the bulb: glycerol influences key stages of lily development

A bulb is a whole plant condensed into an underground organ. A geophyte's bulb comprises both food reserves and important developmental history that may affect its whole growth. In Easter lily (Lilium longiflorum), bulb size is associated with the plant's flowering pathway - vernalization or photoperiod - and also affects sprouting, flower quality and abortion rate. The aim of this study was to investigate the reasons for the major physiological differences between large and small bulbs. Lily bulbs start their development from secondary meristems along the stem, with large bulbs being heavier and bear more scales than small ones. Peeling the outer scales of a large bulb converts its physiological responses into those of a small bulb, implying that the physiological discrepancies in plants developing from large or small bulbs are mediated by factors inherent to the bulb. We therefore performed broad analyses of the metabolite composition in the scales of bulbs subjected to temperature regimes affecting further plant development. We found a striking association between the level of glycerol, a primary metabolite mostly synthesized in the outer scales, and a delay in sprouting and flowering time, and reduction in abortion rate. Exogenous glycerol application to the bulbs before planting corroborated these results. Moreover, transcriptome analyses showed that flowering-promoting gene expression was downregulated in the bulb after glycerol treatment, while potential flowering inhibitor as well as a dormancy-related gene expressions were upregulated. Based on these studies, we postulate that glycerol is a major factor influencing both vegetative and reproductive development in lily.