Miracle-dz/UniFAR-FTUs huggingface dataset:
Modified CLIP score with the albumin-bilirubin grade retains prognostic value in HBV-related hepatocellular carcinoma patients treated with trans-catheter arterial chemoembolization therapy

Background: The Cancer of the Liver Italian Program (CLIP) score is commonly used for prognosis prediction of hepatocellular carcinoma (HCC). The CLIP includes the Child-Pugh grade, which is relatively subjective, for hepatic encephalopathy assessment. A newly developed scoring system called albumin-bilirubin grade (ALBI grade), consists of albumin and bilirubin to assess liver function reserve objectively. Here, we substituted the ALBI grade for the Child-Pugh grade to establish the ALBI-CLIP scoring system and validated its prognostic value in hepatitis B virus (HBV)-related HCC patients treated with trans-catheter arterial chemoembolization (TACE) therapy. Methods: We retrospectively analyzed HBV-related HCC patients who received TACE therapy. Baseline characteristics were collected and evaluated to classify patients according to ALBI-CLIP, CLIP and TNM systems. Univariate analyses using the Kaplan-Meier method and the log-rank test, as well as multivariate analysis using the Cox proportional hazards regression model, were conducted to detect independent prognostic factors for overall survival. Receiver operating characteristic (ROC) curves and a likelihood ratio test (LRT) were both utilized to compare the values of ALBI-CLIP, CLIP and TNM staging systems in predicting survival. Results: With a total of 389 patients included in the current study, 301 (77.4%) and 88 (22.6%) were classified as Child-Pugh grade A and B, respectively. However, 152 (39.1%), 227 (58.4%) and 10 (2.5%) patients were correspondingly classified into ALBI grade 1, 2 and 3. The areas under the curves of ALBI-CLIP, CLIP and TNM systems were 0.804, 0.778 and 0.734, respectively, for predicting 3-month survival; 0.796, 0.778 and 0.733, respectively, for 6-month survival; 0.697, 0.687 and 0.644, respectively, for 1-year survival; and 0.618, 0.612 and 0.569, respectively, for 2-year survival. The LRT indicated that the ALBI-CLIP and the CLIP had similar values of χ2 and Akaike information criterion (AIC) while the TNM system had the smallest χ2 value (χ2 = 12.1, 11.9, 10.5; AIC = 2620.2, 2620.5, 2621.1 for ALBI-CLIP, CLIP and TNM, respectively). Conclusions: In conclusion, our present study suggested that the ALBI-CLIP scoring system retained the prognostic value of the CLIP in HBV-related HCC treated with TACE therapy.
Dominant strictures in primary sclerosing cholangitis: A multicenter survey of clinical definitions and practices

Dominant strictures (DSs) of the biliary tree occur in approximately 50% of patients with primary sclerosing cholangitis (PSC) and may cause significant morbidity. Nevertheless, the definition and management of DSs lacks consensus. We aimed to better understand current perceptions and practices regarding PSC‐associated DSs. We conducted an anonymous, 23‐question, survey‐based study wherein electronic surveys were distributed to 131 faculty in the Division of Gastroenterology and Hepatology at the three Mayo Clinic campuses (Rochester, Scottsdale, and Jacksonville) as well as the affiliated practice network. Responses were aggregated and compared, where applicable, to practice guidelines of the American Association for the Study of Liver Diseases and European Association for the Study of the Liver. A total of 54 faculty (41.2%) completed the survey, of whom 24 (44.4%) were hepatologists, 21 (38.9%) gastroenterologists, and 9 (16.7%) advanced endoscopists. One of the major study findings was that there was heterogeneity among participants' definition, evaluation, management, and follow‐up of DSs in PSC. The majority of participant responses were in accordance with societal practice guidelines, although considerable variation was noted. Conclusion: Despite the prevalence and morbidity of DSs in PSC, clinical perceptions and practices vary widely among hepatologists, gastroenterologists, and advanced endoscopists who manage these patients, even within a single health care system. Further studies are needed to address these variations, develop general and evidence‐based consensus, and increase adherence to societal guidelines. (Hepatology Communications 2018;2:836‐844)
Introducing Transthyretin as a Differentially Expressed Protein in Washing Subtype of Obsessive-Compulsive Disorder

Introduction: Obsessive-Compulsive Disorder (OCD) as one of the important mental problems is valuable topic for proteomic research studies to better understand the underlying mechanisms of this disorder. Methods: In this paper, gel-based proteomic was used to investigate the proteome profile of 16 female patients with OCD, washing subtype before and after treatment with fluoxetine and comparing them with 20 healthy female controls. Results: One of the abnormally expressed protein spots in this study was introduced and examined for protein-protein interaction network analysis via Cytoscape and its plug-ins. Transthyretin (TTR) protein showed significant expression changes (fold change=1.7, P<0.05). While the expression level of TTR is significantly decreased in OCD patients before any treatments, the trend is partially normalized after treatment with fluoxetine in positive responders. Furthermore, TTR interaction profile shows that the proteins interacting with this protein may get affected as this protein expression trend changes in OCD patients. Conclusion: TTR can be considered for further studies to be validated as a potential biomarker for OCD.
Development of Novel Photosensitizer Using the Buddleja officinalis Extract for Head and Neck Cancer

Photodynamic therapy (PDT) is generally safer and less invasive than conventional strategies for head and neck cancer treatment. However, currently available photosensitizers have low selectivity for tumor cells, and the burden and side effects are so great that research is needed to develop safe photosensitizers. In this study, it was confirmed that the Buddleja officinalis (BO) extract, used in the treatment of inflammation and vascular diseases, shows fluorescence when activated by LED light, and, based on this, we aimed to develop a new photosensitive agent suitable for PDT. MTT, Diff-Quick® staining, and DCF-DA were performed to measure the effects of treating head and neck cancer cells with BO extract and 625 nm LED light (BO-PDT). Cell cycle, TUNEL, and western blot assays, as well as acridine orange staining, were performed to explore the mechanism of BO-PDT-induced cell death. We found that when the BO extract was irradiated with 625 nm LED light, it showed sufficient fluorescence and stronger intracellular toxicity and ROS effect than the currently commercially available hematoporphyrin. BO-PDT resulted in a decrease of mTOR activity that was correlated with an increase in the levels of ATG5, beclin-1, and LC3-II, which interfere with the formation of autophagosomes. In addition, BO-PDT induced the activation of PARP and led to an increase in the expression of proapoptotic protein Bax and a decrease in the expression of the antiapoptotic protein Bcl-2. Moreover, BO-PDT has been shown to induce the autophagy pathway 4 h after treatment, while apoptosis was induced 16 h after treatment. Finally, we confirmed that BO-PDT caused cell death of head and neck cancer cells via the intrinsic pathway. Therefore, we suggest that BO extract can be used as a new photosensitizer in PDT of head and neck cancer.
Objectively-Measured Physical Activity and Sedentary Time are Differentially Related to Dietary Fat and Carbohydrate Intake in Children

Background: Research on the clustering of physical activity, sedentary, and dietary intake behaviors in children has relied on retrospective and parent-report measures, which may obscure true associations. The current study combined objectively-measured moderate-to-vigorous intensity physical activity (MVPA) and sedentary time (ST) data from waist-worn accelerometers, with multiple child-report 24-h dietary recalls to assess specific components of dietary intake (i.e., dietary fat, carbohydrates, protein; glycemic load, fruits and vegetables) in children. Methods: Participants (n = 136, ages 8–12 years) wore an accelerometer for 7 days. On two of those days, children completed 24-h recall phone interviews to assess dietary intake. Results: After adjusting for child age, sex, ethnicity, annual household income, and body mass index (BMI) percentile; ST was positively associated with percent dietary fat intake, and negatively associated with percent dietary carbohydrate intake and glycemic load (p's < 0.01). MVPA was positively associated with percent dietary carbohydrate intake and daily glycemic load, and negatively associated with percent dietary fat intake (p's < 0.05). Conclusion: Despite its direct health benefits, physical activity may be associated with consuming greater proportion of total intake from carbohydrates, especially those with a higher glycemic index. Further research is needed to understand the differential implications of these unique behavioral interrelations for diabetes, cardiovascular, and obesity risk.
Improving Simple Models with Confidence Profiles

In this paper, we propose a new method called ProfWeight for transferring information from a pre-trained deep neural network that has a high test accuracy to a simpler interpretable model or a very shallow network of low complexity and a priori low test accuracy. We are motivated by applications in interpretability and model deployment in severely memory constrained environments (like sensors). Our method uses linear probes to generate confidence scores through flattened intermediate representations. Our transfer method involves a theoretically justified weighting of samples during the training of the simple model using confidence scores of these intermediate layers. The value of our method is first demonstrated on CIFAR-10, where our weighting method significantly improves (3-4%) networks with only a fraction of the number of Resnet blocks of a complex Resnet model. We further demonstrate operationally significant results on a real manufacturing problem, where we dramatically increase the test accuracy of a CART model (the domain standard) by roughly 13%.
Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation

Identifying and monitoring locally adaptive genetic variation can have direct utility for conserving species at risk, especially when management may include actions such as translocations for restoration, genetic rescue, or assisted gene flow. However, genomic studies of local adaptation require careful planning to be successful, and in some cases may not be a worthwhile use of resources. Here, we offer an adaptive management framework to help conservation biologists and managers decide when genomics is likely to be effective in detecting local adaptation, and how to plan assessment and monitoring of adaptive variation to address conservation objectives. Studies of adaptive variation using genomic tools will inform conservation actions in many cases, including applications such as assisted gene flow and identifying conservation units. In others, assessing genetic diversity, inbreeding, and demographics using selectively neutral genetic markers may be most useful. And in some cases, local adaptation may be assessed more efficiently using alternative approaches such as common garden experiments. Here, we identify key considerations of genomics studies of locally adaptive variation, provide a road map for successful collaborations with genomics experts including key issues for study design and data analysis, and offer guidelines for interpreting and using results from genomic assessments to inform monitoring programs and conservation actions.
Replicability of Physical Exercise Interventions in Lung Transplant Recipients; A Systematic Review

Introduction: This systematic review aimed to assess the replicability of physical exercise interventions in lung transplantation patients. For replicability we focused on (1) the description of training principles, (2) the description of FITT components and adherence to the interventions, (3) the amount of detailed information given on the physical exercise intervention, and (4) reporting the methodological quality of the included works. Methods: Relevant databases (Medline-Ovid, EMBASE, CINAHL, PsychInfo, Cochrane Library) were searched. Author dyads selected and systematically analyzed the included studies independent from each other. A purpose developed checklist was used to assess the details of the exercise interventions and their methodological quality. Results: From the seven included manuscripts, three described resistance training, one endurance, and three combined training approaches. All manuscripts reported specificity and initial values, six manuscripts mention progression and overload. The exercise principle reversibility was reported once and diminishing returns was not reported at all. All studies reported the type of exercise, three studies reported intensity and one study reported time for training. Not any study completely reported frequency or described adherence to the intervention. Lack of detailed reporting was identified as the cause for murky description of the interventions. The highest score for intervention description was 5 of possible 12 items. Conclusions: Replicability of many exercise interventions in LTX is not warranted due too poor descriptions of important items related to training. In particular there were insufficiently detailed reporting of training principles and FITT components in programs developed for LTX. Future interventions that aim to train LTX patients should spent effort in writing reports in which the intervention is detailed to such an extent that full replicability in clinical settings can be guaranteed.
Expanded Regulatory T Cells Induce Alternatively Activated Monocytes With a Reduced Capacity to Expand T Helper-17 Cells

Regulatory T cells (Tregs) are essential in maintaining peripheral immunological tolerance by modulating several subsets of the immune system including monocytes. Under inflammatory conditions, monocytes migrate into the tissues, where they differentiate into dendritic cells or tissue-resident macrophages. As a result of their context-dependent plasticity, monocytes have been implicated in the development/progression of graft-vs-host disease (GvHD), autoimmune diseases and allograft rejection. In the last decade, Tregs have been exploited for their use in cell therapy with the aim to induce tolerance after solid organ transplantation and for the treatment of autoimmune diseases and GvHD. To date, safety and feasibility of Treg infusion has been demonstrated; however, many questions of how these cells induce tolerance have been raised and need to be answered. As monocytes constitute the major cellular component in inflamed tissues, we have developed an in vitro model to test how Tregs modulate their phenotype and function. We demonstrated that expanded Tregs can drive monocytes toward an alternatively activated state more efficiently than freshly isolated Tregs. The effect of expanded Tregs on monocytes led to a reduced production of pro-inflammatory cytokines (IL-6 and tumor necrosis factor-α) and NF-κB activation. Furthermore, monocytes co-cultured with expanded Tregs downregulated the expression of co-stimulatory and MHC-class II molecules with a concomitant upregulation of M2 macrophage specific markers, CD206, heme oxygenase-1, and increased interleukin-10 production. Importantly, monocytes co-cultured with expanded Tregs showed a reduced capacity to expand IL-17-producing T cells compared with monocyte cultured with freshly isolated Tregs and conventional T cells. The capacity to decrease the expansion of pro-inflammatory Th-17 was not cytokine mediated but the consequence of their lower expression of the co-stimulatory molecule CD86. Our data suggest that expanded Tregs have the capacity to induce phenotypical and functional changes in monocytes that might be crucial for tolerance induction in transplantation and the prevention/treatment of GvHD and autoimmune diseases.
Towards Explainable and Controllable Open Domain Dialogue Generation with Dialogue Acts

We study open domain dialogue generation with dialogue acts designed to explain how people engage in social chat. To imitate human behavior, we propose managing the flow of human-machine interactions with the dialogue acts as policies. The policies and response generation are jointly learned from human-human conversations, and the former is further optimized with a reinforcement learning approach. With the dialogue acts, we achieve significant improvement over state-of-the-art methods on response quality for given contexts and dialogue length in both machine-machine simulation and human-machine conversation.
A \(\boldsymbol{\phi }\) -Competitive Algorithm for Scheduling Packets with Deadlines

In the online packet scheduling problem with deadlines (PacketScheduling, for short), the goal is to schedule transmissions of packets that arrive over time in a network switch and need to be sent across a link. Each packet has a deadline, representing its urgency, and a non-negative weight, that represents its priority. Only one packet can be transmitted in any time slot, so, if the system is overloaded, some packets will inevitably miss their deadlines and be dropped. In this scenario, the natural objective is to compute a transmission schedule that maximizes the total weight of packets which are successfully transmitted. The problem is inherently online, with the scheduling decisions made without the knowledge of future packet arrivals. The central problem concerning PacketScheduling, that has been a subject of intensive study since 2001, is to determine the optimal competitive ratio of online algorithms, namely the worst-case ratio between the optimum total weight of a schedule (computed by an offline algorithm) and the weight of a schedule computed by a (deterministic) online algorithm. We solve this open problem by presenting a $\phi$-competitive online algorithm for PacketScheduling (where $\phi\approx 1.618$ is the golden ratio), matching the previously established lower bound.
Demographic characteristics and the first program of colorectal cancer (CRC) screening in north of Iran (2016).

Background Colorectal cancer (CRC) is one of the most common types of gastrointestinal cancers. This study aimed to determine the demographic characteristics and their relationships with the results of the first screening program for CRC in people over 50 years old in northern Iran. Methods This cross-sectional study was conducted in 2016 on 924 eligible people over 50 years old. Initial screening was done by IFOBT and then colonoscopy was performed if the results were positive. The demographic characteristics of individuals including age, sex, place of residence, marital status, body mass index (BMI) and education level were investigated with the results of the colonoscopy and the test results. Results The mean age of participants was 59.38 years, and the participation of women (57.0%) and rural residents (54.2%) were higher in the screening program. According to the demographic variables, age was considered as a strong independent predictor variable, so that the prevalence of positive test results was more than 2 times higher in subjects older than 70 compared with subjects aged ≤60 (OR =2.05; 95% CI, 1.18-3.55, P=0.010). Also, the chance of positive test result in the age group ≤55 years old was 23%, with an increase of 64% in the age group above 75 years (P<0.001). Among the positive test subjects, 118 cases underwent colonoscopy. Conclusions The prevalence of IFOBT positivity was increased with age. Therefore, given the aging population of the country, it is recommended to emphasize on the screening of older people in the general population.
Powerful anti-colon cancer effect of modified nanoparticle-mediated IL-15 immunogene therapy through activation of the host immune system

Rationale: Colorectal cancer (CRC) is the third most commonly diagnosed cancer around the world. Over the past several years, immunotherapy has demonstrated considerable clinical benefit in CRC therapy, and the number of immunologic therapies for cancer treatment continues to climb each year. Interleukin-15 (IL15), a potent pro-inflammatory cytokine, has emerged as a candidate immunomodulator for the treatment of CRC. Methods: In this study, we developed a novel gene delivery system with a self-assembly method using DOTAP and MPEG-PLA (DMA) to carry pIL15, denoted as DMA-pIL15 which was used to treat tumor-bearing mice. Results: Supernatant from lymphocytes treated with supernatant derived from CT26 cells transfected with DMA-pIL15 inhibited the growth of CT26 cells and induced cell apoptosis in vitro. Treatment of tumor-bearing mice with DMA-pIL15 complex significantly inhibited tumor growth in both subcutaneous and peritoneal models in vivo by inhibiting angiogenesis, promoting apoptosis, and reducing proliferation through activation of the host immune system. Conclusion: The IL-15 plasmid and DMA complex showed promise for treating CRC clinically as an experimental new drug.
Middle Cerebral Artery Pulsatility Index as Predictor of Cognitive Impairment in Hypertensive Patients

Background: Cognitive impairment is a manifestation of cerebrovascular disease regarding hypertension and other degenerative diseases which has become a global health issue due to increased life expectancy. Recently, the gold standard used for diagnosing vascular cognitive impairment (VCI) has required a combination of the neurophysiological approach and magnetic resonance imaging (MRI). The Neurosonological approach, involving measuring the pulsatility index (PI) of the middle cerebral artery (MCA) using Trans Cranial Doppler (TCD), can hopefully be used as an affordable alternative predictor of VCI in patients with hypertension. Methods: A cross-sectional study was conducted at the Outpatient Clinic of the Department of Neurology in Ciptomangunkusumo Hospital, Jakarta. Sixty-six hypertensive subjects with no macrovascular complication were selected and screened using the Montreal Cognitive Assesment-Indonesia version (MoCA-Ina) to determine their cognitive status. Subjects were categorized into two groups; subjects with scores ≥26 were classified as the normal cognitive group, while subjects with scores <26 were classified as the cognitive impairment group. Both groups then underwent TCD examination to determine bilateral MCA PI. Results: There was a significant difference between MCA PI in both groups; it was higher in the cognitive impairment group than normal group (p < 0.001). Subjects with an increased left MCA PI were more likely to suffer cognitive impairment than those with an increased right MCA PI. Conclusion: MCA PI can be used as a predictor for cognitive impairment in hypertensive subjects.