Miracle-dz/UniFAR-FTUs huggingface dataset:
A Research on Treatment of Chromium Containing Wastewater with Ultrasonic-Ferrite Method

The chromium containing wastewater was treated with ultrasonic-ferrite method,and the effects of feeding ratio(nFe2+∶nCr(VI)),pH value,H2O2dosage,initial mass concentration of Cr(VI),ultrasonic radiation time,etc.on the removal rate of Cr(VI)were investigated.The removal efficiency was evaluated according to absorbance,and on this basis the best operating conditions were sought.Chromium removal efficiency could be more than 99 % and the ferrite magnetism would be the strongest when feeding ratio is 7.5,pH value 8.0~9.0,H2O2dosage 15mg/L and ultrasonic radiation time 30minutes.The experiment also shows that the higher the initial mass concentration of Cr(VI),the greater the chromium removal rate;and the wastewater treated with this method could meet the national discharge standards.The treatment of chromium containing wastewater was influenced by Cu2+and Zn2+. In addition,ultrasonic waves have a stronger promoting effect on the removal of chromium with ferrite.
Pharmit: interactive exploration of chemical space

Pharmit (http://pharmit.csb.pitt.edu) provides an online, interactive environment for the virtual screening of large compound databases using pharmacophores, molecular shape and energy minimization. Users can import, create and edit virtual screening queries in an interactive browser-based interface. Queries are specified in terms of a pharmacophore, a spatial arrangement of the essential features of an interaction, and molecular shape. Search results can be further ranked and filtered using energy minimization. In addition to a number of pre-built databases of popular compound libraries, users may submit their own compound libraries for screening. Pharmit uses state-of-the-art sub-linear algorithms to provide interactive screening of millions of compounds. Queries typically take a few seconds to a few minutes depending on their complexity. This allows users to iteratively refine their search during a single session. The easy access to large chemical datasets provided by Pharmit simplifies and accelerates structure-based drug design. Pharmit is available under a dual BSD/GPL open-source license.
Integrating Telehealth Care-Generated Data With the Family Practice Electronic Medical Record: Qualitative Exploration of the Views of Primary Care Staff

Background Telehealth care is increasingly being employed in the management of long-term illness. Current systems are largely managed via “stand-alone” websites, which require additional log-ons for clinicians to view their patients’ symptom records and physiological measurements leading to frustrating delays and sometimes failure to engage with the record. However, there are challenges to the full integration of patient-acquired data into family physicians’ electronic medical records (EMR) in terms of reliability, how such data can best be summarized and presented to avoid overload to the clinicians, and how clarity of responsibility is managed when multiple agencies are involved. Objective We aimed to explore the views of primary care clinicians on the acceptability, clinical utility, and, in particular, the benefits and risks of integrating patient-generated telehealth care data into the family practice EMR and to explore how these data should be summarized and presented in order to facilitate use in routine care. Methods In our qualitative study, we carried out semi-structured interviews with clinicians with experience of and naïve to telehealth care following demonstration of pilot software, which illustrated various methods by which data could be incorporated into the EMR. Results We interviewed 20 clinicians and found 2 overarching themes of “workload” and “safety”. Although clinicians were largely positive about integrating telehealth care data into the EMR, they were concerned about the potential increased workload and safety issues, particularly in respect to error due to data overload. They suggested these issues could be mitigated by good system design that summarized and presented data such that they facilitated seamless integration with clinicians’ current routine processes for managing data flows, and ensured clear lines of communication and responsibility between multiple professionals involved in patients’ care. Conclusions Family physicians and their teams are likely to be receptive to and see the benefits of integrating telehealth-generated data into the EMR. Our study identified some of the key challenges that must be overcome to facilitate integration of telehealth care data. This work particularly underlines the importance of actively engaging with clinicians to ensure that systems are designed that align well with existing practice data-flow management systems and facilitate safe multiprofessional patient care.
Unbiased compound-protein interface mapping and prediction of chemoresistance loci through forward genetics in haploid stem cells

Forward genetic screens in haploid mammalian cells have recently emerged as powerful tools for the discovery and investigation of recessive traits. Use of the haploid system provides unique genetic tractability and resolution. Upon positive selection, these screens typically employ analysis of loss-of-function (LOF) alleles and are thus limited to non-essential genes. Many relevant compounds, including anti-cancer therapeutics, however, target essential genes, precluding positive selection of LOF alleles. Here, we asked whether the use of random and saturating chemical mutagenesis might enable screens that identify essential biological targets of toxic compounds. We compare and contrast chemical mutagenesis with insertional mutagenesis. Selecting mutagenized cells with thapsigargin, an inhibitor of the essential Ca2+ pump SERCA2, insertional mutagenesis retrieved cell clones overexpressing SERCA2. With chemical mutagenesis, we identify six single amino acid substitutions in the known SERCA2-thapsigargin binding interface that confer drug resistance. In a second screen, we used the anti-cancer drug MG132/bortezomib (Velcade), which inhibits proteasome activity. Using chemical mutagenesis, we found 7 point mutations in the essential subunit Psmb5 that map to the bortezomib binding surface. Importantly, 4 of these had previously been identified in human tumors with acquired bortezomib resistance. Insertional mutagenesis did not identify Psmb5 in this screen, demonstrating the unique ability of chemical mutagenesis to identify relevant point mutations in essential genes. Thus, chemical mutagenesis in haploid embryonic stem cells can define the interaction of toxic small molecules with essential proteins at amino acid resolution, fully mapping small molecule-protein binding interfaces.
Akt‐dependent and Akt‐independent pathways are involved in protein synthesis activation during reloading of disused soleus muscle

Introduction: The purpose of our study was to assess the contribution of insulin growth factor‐1–dependent and phosphatidic acid‐dependent signaling pathways to activation of protein synthesis (PS) in rat soleus muscle during early recovery from unloading. Methods: Wistar rats were divided into: Control, 14HS [14‐day hindlimb suspension (HS)], 3R+placebo (3‐day reloading + saline administration), 3R+Wort (3‐day reloading + wortmannin administration), 3R+But (3‐day reloading + 1‐butanol administration). SUnSET and Western blot analyses were used in this study. Results: Wortmannin and 1‐butanol induced a decrease in protein kinase B (phospho‐Akt) and the rate of PS (P < 0.05) versus Control. In 3R+placebo and 3R+Wort, phosphorylation of glycogen synthase kinase 3 beta (phospho‐GSK‐3β) was increased versus Control (P < 0.05). Wortmannin administration during reloading did not alter phospho‐p70S6K (70 kDa ribosomal protein S6 kinase) versus 3R+placebo. In 3R+But, there was a decline in phospho‐GSK‐3β versus 3R+placebo and Control. In 3R+But, there was a decrease in phopho‐p70S6K (P < 0.05) versus 3R+placebo. Conclusions: These results suggest that PS activation during 3‐day reloading following 14HS involves both Akt‐dependent and Akt‐independent pathways. Muscle Nerve 55: 393–399, 2017
A new deep brain stimulation waveform based on PWM

This paper proposes a non-periodic shape optimization based on PWM principle to identify the optimal parameters of deep brain stimulation (DBS) waveforms. A computational model characterizing Parkinson's disease (PD) is introduced. When PWM DBS is injected into the networks, the tonic rhythm output of GPi neurons could restore the thalamic relay properties. By comparing with the periodic rectangular waveforms, we demonstrate the view that the PWM waveforms can not only guarantee the reliability, but also can decrease energy requirements of stimulation in vivo, that means, it can increase the lifetime of the DBS electrodes, decrease the stimulation-induced tissue damage, then improve the quality of life for PD patient.
An O(n\log n)-Time Algorithm for the k-Center Problem in Trees

We consider a classical k-center problem in trees. Let T be a tree of n vertices and every vertex has a nonnegative weight. The problem is to find k centers on the edges of T such that the maximum weighted distance from all vertices to their closest centers is minimized. Megiddo and Tamir (SIAM J. Comput., 1983) gave an algorithm that can solve the problem in O(n log^2 n) time by using Cole's parametric search. Since then it has been open for over three decades whether the problem can be solved in O(n log n) time. In this paper, we present an O(n log n) time algorithm for the problem and thus settle the open problem affirmatively.
Parsimonious User and Group Profiling in Venue Recommendation

This paper presents the University of Amsterdam’s participation in the TREC 2015 Contextual Suggestion Track. Creating e↵ective profiles for both users and contexts is the main key to build an e↵ective contextual suggestion system. To address these issues, we investigate building users’ and groups’ profiles for e↵ective contextual personalization and customization. Our main aim is to answer the questions: How to build a user-specific profile that penalizes terms having high probability in negative language models? Can parsimonious language models improve user and context profile’s e↵ectiveness? How to combine both models and benefit from both a contextual customization using contextual group profiles and a contextual personalization using users profiles? Our main findings are the following: First, although using parsimonious language model leads to a more compact language model as users’ profiles, the personalization performance is as good as using standard language models for building users’ profiles. Second, we extensively analyze e↵ectiveness of three di↵erent approaches in taking the negative profiles into account, which improves performance of contextual suggestion models that just uses positive profiles. Third, we learn an e↵ective model for contextual customization and analyze the importance of different contexts in contextual suggestion task. Finally, we propose a linear combination of contextual customization and personalization, which improves the performance of contextual suggestion using either contextual customization or personalization based on all the common used IR metrics.
Human TERT promoter mutation enables survival advantage from MGMT promoter methylation in IDH1 wild-type primary glioblastoma treated by standard chemoradiotherapy

Background Promoter mutation in the human telomerase reverse transcriptase gene (hTERT) occurs in ~75% of primary glioblastoma (GBM). Although the mutation appears to upregulate telomerase expression and contributes to the maintenance of telomere length, its clinical significance remains unclear. Methods We performed hTERT promoter genotyping on 303 isocitrate dehydrogenase 1 wild-type GBM tumors treated with standard chemoradiotherapy. We also stratified 190 GBM patients from the database of The Cancer Genome Atlas (TCGA) by hTERT gene expression. We analyzed overall and progression-free survival by Kaplan-Meier and Cox regression. Results We detected hTERT promoter mutation in 75% of the patients. When included as the only biomarker, hTERT mutation was not prognostic in our patient cohort by Cox regression analysis. However, when hTERT and O6-DNA methylguanine-methyltransferase (MGMT) were included together, we observed an interaction between these 2 factors. To further investigate this interaction, we performed pairwise comparison of the 4 patient subcohorts grouped by hTERT-MGMT status (MUT-M, WT-M, MUT-U, and WT-U). MGMT methylated patients showed improved survival only in the presence of hTERT promoter mutation: MUT-M versus MUT-U (overall survival of 28.3 vs 15.9 mos, log-rank P < .0001 and progression-free survival of 15.4 vs 7.86 mo, log-rank P < .0001). These results were confirmed by Cox analyses. Analogously, the cohort from TCGA demonstrated survival benefit of MGMT promoter methylation only in patients with high hTERT expression. In addition, hTERT mutation was negatively prognostic in our MGMT unmethylated patients, while the analogous association with high expression was not observed in the cohort from TCGA. Conclusion The prognostic influence of MGMT promoter methylation depends on hTERT promoter mutation. This interaction warrants further mechanistic investigation.
Simple screening tools to identify limited health literacy in a low-income patient population

Abstract Adults with limited health literacy have difficulty managing chronic conditions, higher hospitalization rates, and more healthcare expenditures. Simple screening tools have been developed, but limited work has evaluated instruments among low-income populations. This study assessed health literacy among primary care patients of a federally qualified health center, and compared a single screening question about perceived difficulty completing medical forms. A cross-sectional survey was administered to English-speaking patients ≥40 years. Both the Newest Vital Sign (NVS), a 6-item questionnaire, and a single-item screening question about perceived difficulty with completing medical forms, assessed health literacy. Logistic regression was used to identify predictors of inadequate health literacy and receiver operator curves compared the NVS and single-item question. Participants (n = 406) were, on average, aged 58.5 years (±11.3), 72.2% female, and identified as Hispanic/Latino (19.2%), non-Hispanic white (31.0%), non-Hispanic black (40.9%), or other (8.9%). Of the 406 participants, 335 (82.5%) completed the NVS. Patients who declined NVS were more likely to be older (P < .001) and male (P = .01). Only 13.7% had adequate health literacy. Older adults, Hispanic and non-Hispanic black patients, patients with missed office visits, and those reporting less confidence completing medical forms were significantly more likely to have inadequate health literacy. Perceived confidence completing medical forms demonstrated low sensitivity but high specificity at multiple thresholds. This is the first investigation to compare the NVS and confidence completing medical forms question. Many patients declined health literacy assessments, but health literacy screening may identify patients who need additional health education and resources.
MEK and TAK1 Regulate Apoptosis in Colon Cancer Cells with KRAS-Dependent Activation of Proinflammatory Signaling

MEK inhibitors have limited efficacy in treating RAS–RAF–MEK pathway–dependent cancers due to feedback pathway compensation and dose-limiting toxicities. Combining MEK inhibitors with other targeted agents may enhance efficacy. Here, codependencies of MEK, TAK1, and KRAS in colon cancer were investigated. Combined inhibition of MEK and TAK1 potentiates apoptosis in KRAS-dependent cells. Pharmacologic studies and cell-cycle analyses on a large panel of colon cancer cell lines demonstrate that MEK/TAK1 inhibition induces cell death, as assessed by sub-G1 accumulation, in a distinct subset of cell lines. Furthermore, TAK1 inhibition causes G2–M cell-cycle blockade and polyploidy in many of the cell lines. MEK plus TAK1 inhibition causes reduced G2–M/polyploid cell numbers and additive cytotoxic effects in KRAS/TAK1-dependent cell lines as well as a subset of BRAF-mutant cells. Mechanistically, sensitivity to MEK/TAK1 inhibition can be conferred by KRAS and BMP receptor activation, which promote expression of NF-κB-dependent proinflammatory cytokines, driving tumor cell survival and proliferation. MEK/TAK1 inhibition causes reduced mTOR, Wnt, and NF-κB signaling in TAK1/MEK-dependent cell lines concomitant with apoptosis. A Wnt/NF-κB transcriptional signature was derived that stratifies primary tumors into three major subtypes: Wnt-high/NF-κB-low, Wnt-low/NF-κB-high and Wnt-high/NF-κB-high, designated W, N, and WN, respectively. These subtypes have distinct characteristics, including enrichment for BRAF mutations with serrated carcinoma histology in the N subtype. Both N and WN subtypes bear molecular hallmarks of MEK and TAK1 dependency seen in cell lines. Therefore, N and WN subtype signatures could be utilized to identify tumors that are most sensitive to anti-MEK/TAK1 therapeutics. Implications: This study describes a potential therapeutic strategy for a subset of colon cancers that are dependent on oncogenic KRAS signaling pathways, which are currently difficult to block with selective agents. Mol Cancer Res; 14(12); 1204–16. ©2016 AACR.
LassoProt: server to analyze biopolymers with lassos

The LassoProt server, http://lassoprot.cent. uw.edu. pl/, enables analysis of biopolymers with entangled configurations called lassos. The server offers various ways of visualizing lasso configurations, as well as their time trajectories, with all the results and plots downloadable. Broad spectrum of applications makes LassoProt a useful tool for biologists, biophysicists, chemists, polymer physicists and mathematicians. The server and our methods have been validated on the whole PDB, and the results constitute the database of proteins with complex lassos, supported with basic biological data. This database can serve as a source of information about protein geometry and entanglement-function correlations, as a reference set in protein modeling, and for many other purposes.
Perceived role and its enhancing factors among the village health volunteers regarding malaria control in rural myanmar

Background: Village health volunteers (VHVs) are key agents for malaria control in community. The Myanmar Medical Association-Malaria (MMA-Malaria) Project has promoted effective malaria control in endemic and high-risk townships by supporting roles of VHVs. Objectives: To assess the roles of VHVs on malaria control and factors enhancing their roles in rural Myanmar. Methods: A cross-sectional study was conducted in five townships where the MMA-Malaria Project has been implemented. One hundred and fifty VHVs were sampled from five townships by simple random sampling. Data were collected by trained interviewers using structured questionnaires, which covered sociodemographic, supportive, motivational factors, and roles of malaria control. Studied variables were described by proportions, means, and standard deviations and were analyzed for their association by odds ratio with 95% confidence interval and Chi-square tests. Results: Most of VHVs (96%) expected to demonstrate good roles on malaria control, but only 44.0% exhibited current roles at a good level. Factors enhancing their roles were female (P = 0.037), family income ≥50,001 kyat/month (P < 0.015), time serving as a volunteer 1–2 years (P = 0.006), good knowledge of malaria control (P < 0.001), good family support (P < 0.001), good community support (P < 0.001), and good motivational factors (P = 0.002). Conclusion: VHVs are key agents for malaria control in community. Most of VHVs expected to demonstrate good roles on malaria control, but less than half of them exhibited current roles at a good level. The systems and program for improving VHVs’ knowledge, encouraging family and community support, and promoting motivation are essential for their better roles.
On-chip dual-comb source for spectroscopy

A compact, integrated dual-comb source is developed on a single chip to demonstrate fast, real-time spectroscopy of materials. Dual-comb spectroscopy is a powerful technique for real-time, broadband optical sampling of molecular spectra, which requires no moving components. Recent developments with microresonator-based platforms have enabled frequency combs at the chip scale. However, the need to precisely match the resonance wavelengths of distinct high quality-factor microcavities has hindered the development of on-chip dual combs. We report the simultaneous generation of two microresonator combs on the same chip from a single laser, drastically reducing experimental complexity. We demonstrate broadband optical spectra spanning 51 THz and low-noise operation of both combs by deterministically tuning into soliton mode-locked states using integrated microheaters, resulting in narrow (<10 kHz) microwave beat notes. We further use one comb as a reference to probe the formation dynamics of the other comb, thus introducing a technique to investigate comb evolution without auxiliary lasers or microwave oscillators. We demonstrate high signal-to-noise ratio absorption spectroscopy spanning 170 nm using the dual-comb source over a 20-μs acquisition time. Our device paves the way for compact and robust spectrometers at nanosecond time scales enabled by large beat-note spacings (>1 GHz).
Understanding Type 2 Diabetes

Purpose The purpose of this study was to examine the relationship between psychological and social factors and diabetes outcomes in people with type 2 diabetes and their family members. Methods A total of 153 patients with type 2 diabetes were assessed at a diabetes outpatient clinic and postal questionnaires were sent to nominated family members. The measures examined were diabetes knowledge, social support, well-being, and illness perceptions. Results When compared with those with diabetes, family members reported lower positive well-being and lower levels of satisfaction with support. They also perceived diabetes as a more cyclical illness, which was controlled more by treatment than by the individual. Family members also reported that the person with diabetes was more emotionally distressed and knew more about diabetes than the patient had actually reported himself or herself. There were no differences between the family members of those in good or poor glycaemic control. Conclusions This study reinforces the importance of understanding social context and illness beliefs in diabetes management. It also highlights the potential for including family members in discussions and education about diabetes management.