Miracle-dz/UniFAR-FTUs huggingface dataset:
Standardized cancer incidence disparities in Upper Manhattan New York City neighborhoods: the role of race/ethnicity, socioeconomic status, and known risk factors

We examined the effects of race/ethnicity and neighborhood, a proxy of socioeconomic status, on cancer incidence in New York City neighborhoods: East Harlem (EH), Central Harlem (CH), and Upper East Side (UES). In this ecological study, Community Health Survey data (2002–2006) and New York State Cancer Registry incidence data (2007–2011) were stratified by sex, age, race/ethnicity, and neighborhood. Logistic regression models were fitted to each cancer incidence rate with race/ethnicity, neighborhood, and Community Health Survey-derived risk factors as predictor variables. Neighborhood was significantly associated with all cancers and 14 out of 25 major cancers. EH and CH residence conferred a higher risk of all cancers compared with UES (OR=1.34, 95% CI 1.07–1.68; and OR=1.39, 95% CI 1.12–1.72, respectively). The prevalence of diabetes and tobacco smoking were the largest contributors toward high cancer rates. Despite juxtaposition and similar proximity to medical centers, cancer incidence disparities persist among EH, CH, and UES neighborhoods. Targeted, neighborhood-specific outreach may aid in reducing cancer incidence rates.
Advances in sarcoma diagnostics and treatment

The heterogeneity of sarcomas with regard to molecular genesis, histology, clinical characteristics, and response to treatment makes management of these rare yet diverse neoplasms particularly challenging. This review encompasses recent developments in sarcoma diagnostics and treatment, including cytotoxic, targeted, epigenetic, and immune therapy agents. In the past year, groups internationally explored the impact of adding mandatory molecular testing to histological diagnosis, reporting some changes in diagnosis and/or management; however, the impact on outcomes could not be adequately assessed. Transcriptome sequencing techniques have brought forward new diagnostic tools for identifying fusions and/or characterizing unclassified entities. Next-generation sequencing and advanced molecular techniques were also applied to identify potential targets for directed and epigenetic therapy, where preclinical studies reported results for agents active within the receptor tyrosine kinase, mTOR, Notch, Wnt, Hedgehog, Hsp90, and MDM2 signaling networks. At the level of clinical practice, modest developments were seen for some sarcoma subtypes in conventional chemotherapy and in therapies targeting the pathways activated by various receptor tyrosine kinases. In the burgeoning field of immune therapy, sarcoma work is in its infancy; however, elaborate protocols for immune stimulation are being explored, and checkpoint blockade agents advance from preclinical models to clinical studies.
Multi-level pedagogical model for the personalization of pedagogical strategies in intelligent tutoring systems

Pedagogic strategies are action plans designed to manage issues related to sequencing and content organization, specifying learning activities, and deciding how to deliver content and activities in teaching processes. In this paper, we present an approach to personalization of pedagogical strategies in Intelligent Tutoring Systems using pedagogical knowledge rules in a Web environment. The adaptation of pedagogical strategies is made based on a multilevel pedagogical model. An Intelligent Tutoring Systems called FUNPRO was developed to validate the multilevel pedagogical model. The results of empirical tests show that the multilevel pedagogical model enables FUNPRO to improve the process of personalization of pedagogical strategies, due to the reduction of inappropriate recommendations.
Dual Targeting of Epithelial Ovarian Cancer Via Folate Receptor α and the Proton-Coupled Folate Transporter with 6-Substituted Pyrrolo[2,3-d]pyrimidine Antifolates

Folate uptake in epithelial ovarian cancer (EOC) involves the reduced folate carrier (RFC) and the proton-coupled folate transporter (PCFT), both facilitative transporters and folate receptor (FR) α. Although in primary EOC specimens, FRα is widely expressed and increases with tumor stage, PCFT was expressed independent of tumor stage (by real-time RT-PCR and IHC). EOC cell line models, including cisplatin sensitive (IGROV1 and A2780) and resistant (SKOV3 and TOV112D) cells, expressed a 17-fold range of FRα and similar amounts (within ∼2-fold) of PCFT. Novel 6-substituted pyrrolo[2,3-d]pyrimidine thienoyl antifolates AGF94 and AGF154 exhibited potent antiproliferative activities toward all of the EOC cell lines, reflecting selective cellular uptake by FRα and/or PCFT over RFC. When IGROV1 cells were pretreated with AGF94 at pH 6.8, clonogenicity was potently inhibited, confirming cell killing. FRα was knocked down in IGROV1 cells with lentiviral shRNAs. Two FRα knockdown clones (KD-4 and KD-10) showed markedly reduced binding and uptake of [3H]folic acid and [3H]AGF154 by FRα, but maintained high levels of [3H]AGF154 uptake by PCFT compared to nontargeted control cells. In proliferation assays, KD-4 and KD-10 cells preserved in vitro inhibition by AGF94 and AGF154, compared to a nontargeted control, attributable to residual FRα- and substantial PCFT-mediated uptake. KD-10 tumor xenografts in severe-compromised immune-deficient mice were likewise sensitive to AGF94. Collectively, our results demonstrate the substantial therapeutic potential of novel 6-substituted pyrrolo[2,3-d]pyrimidine antifolates with dual targeting of PCFT and FRα toward EOCs that express a range of FRα, along with PCFT, as well as cisplatin resistance. Mol Cancer Ther; 16(5); 819–30. ©2017 AACR.
Baseline energy modelling in an educational building campus for measurement and verification

Universities contain a lot of buildings that is having different behaviour towards energy consumption. The behaviour of the educational building is depending on lecture period and non-lecture period. The change of behaviour may affect the energy consumption of the particular buildings. As a result, it creates a lot of uncertainties on the variables that affect the energy consumption during lecture period and non-lecture period. Variables selection is very important in order to create baseline energy models for educational buildings because it will affect the calculation of energy savings. Thus, this paper intends to investigate the variables that effecting the energy consumption in academic building during non-lecture period by using single and multiple regression method. The results from the regression method will be used to create a baseline energy model for the educational buildings. It is hoped that from this studies the variables that affecting the energy consumption of educational buildings can be identified and baseline energy model for educational buildings can be modelled with a minimal error.
Conditional access smart meter privacy based on multi-resolution wavelet analysis

Smart Metering is an important component of Smart Grids. Detailed load profiles are available through smart metering at a high resolution. Load profiles allow inferring detailed information on the end user by non-intrusive load monitoring. Therefore, these load profiles need to be regarded as sensitive data, and treated with security and privacy in mind. We propose a method that allows conditional access to different resolution levels of the load data, allowing access on a "need-to-know" basis only. For this purpose, a multiresolution representation of the load data is created using the simple Haar wavelet transform. Securing the portions of the wavelet representation pertaining to each resolution with a unique key allows to implement conditional access for smart meter data.
The Effects of Enhanced Compiler Error Messages on a Syntax Error Debugging Test

There is an active strand of research in the literature exploring the effects of Enhanced Compiler Error Messages on student programming behavior, however many results seem conflicting. This is compounded by the fact that directly comparing these results is difficult as these studies utilize different metrics, and what metrics are best suited to measure the effects of enhanced compiler error messages is not known. Common to most studies to-date is that the metrics employed measure how many errors students produce, and/or rectify while writing programs. This study takes a different approach by measuring how many pre-existing syntax errors are rectified by students while debugging programs. Specifically, we measured the effect of enhanced compiler error messages in an empirical control/intervention experiment where students were given the task of removing syntax errors from non-compiling source code they did not write. We find a significant positive effect on the overall number of errors rectified, as well as the number of certain specific error types, but no significant effect on the number of non-compiling submissions or student scores. These results (in different ways) support the findings of several recent studies and suggest that their results may not be as conflicting as they seem. This is evidence that enhanced error messages may be effective, but also that the signal of these effects are relatively weak, indicating that how and what is measured when attempting to observe these effects is important.
Impact of adjuvant hysterectomy on prognosis in patients with locally advanced cervical cancer treated with concurrent chemoradiotherapy: a meta-analysis

Objective Few data exist regarding adjuvant hysterectomy (AH) in locally advanced cervical cancer (LACC) patients treated with chemoradiotherapy. We investigated the effect of AH on prognosis in LACC patients, through meta-analysis. Methods EMBASE and MEDLINE databases and the Cochrane Library were searched for published studies comparing LACC patients who received AH after chemoradiotherapy with those who did not, through April 2016. Endpoints were mortality and recurrence rates. For pooled estimates of the effect of AH on mortality/recurrence, random- or fixed-effects meta-analytical models were used. Results Two randomized trials and six observational studies (AH following chemoradiotherapy, 630 patients; chemoradiotherapy, 585 patients) met our search criteria. Fixed-effects model-based meta-analysis indicated no significant difference in mortality between the groups (odds ratio [OR]=1.01; 95% confidence interval [CI]=0.58–1.78; p=0.968) with low cross-study heterogeneity (p=0.73 and I2=0.0). This pattern was observed in subgroup analysis for study design, radiation type, response after chemoradiotherapy, and hysterectomy type. The pooled OR for AH and recurrence was 0.59 (95% CI=0.44–0.79; p<0.05) with low cross-study heterogeneity (p=0.29 and I2=17.8), favoring the AH group. However, this pattern was not observed in the subgroup analysis for the randomized trials. There was no evidence of publication bias. Conclusion In this meta-analysis, AH following chemoradiotherapy did not improve survival in patients with LACC, although it seemed to reduce the risk of recurrence. Concerning the significant morbidity of AH after chemoradiotherapy, routine use of AH should be avoided.
Equidistributions of Mahonian Statistics over Pattern Avoiding Permutations

A Mahonian d-function is a Mahonian statistic that can be expressed as a linear combination of vincular pattern statistics of length at most d. Babson and Steingrimsson classified all Mahonian 3-functions up to trivial bijections and identified many of them with well-known Mahonian statistics in the literature. We prove a host of Mahonian 3-function equidistributions over pattern avoiding sets of permutations. Tools used include block decomposition, Dyck paths and generating functions.
Incidence of spontaneous lymphomas in non-experimental NOD/Shi-scid, IL-2Rγnull (NOG) mice

Severely immunodeficient NOD/Shi-scid, IL-2Rγnull (NOG) mice provide an in vivo model for human cell/tissue transplantation studies. NOG mice were established by combining interleukin-2 receptor-γ chain knockout mice and NOD/Shi-scid mice. They exhibit a high incidence of thymic lymphomas and immunoglobulin (Ig) leakiness. In this study, we assessed the incidence of malignant lymphomas and the occurrence of leakiness in 2,184 non-experimental NOG retired breeder mice aged 16–40 weeks. We established that the total incidence of lymphomas was only 0.60% (13/2,184). Most lymphomas (10/13) occurred in female mice by the age of around 25 weeks. No mice developed Ig leakiness. All lymphomas were derived from the thymus, and consisted mainly of CD3-positive and CD45R-negative lymphoblastic-like cells. Therefore, based on the absence of Ig leakiness and a very low incidence of lymphomas, including thymic lymphomas, NOG mice may be useful in regeneration medicine for xenotransplantation of human embryonic stem (ES) cells or induced pluripotent stem (iPS) cells, and in transplantation experiments involving tumor cells.
Advancements in Irreversible Electroporation for the Treatment of Cancer

Irreversible electroporation has recently emerged as an effective focal ablation technique. When performed clinically, the procedure involves placing electrodes into, or around, a target tissue and applying a series of short, but intense, pulsed electric fields. Oftentimes, patient specific treatment plans are employed to guide procedures by merging medical imaging with algorithms for determining the electric field distribution in the tissue. The electric field dictates treatment outcomes by increasing a cell’s transmembrane potential to levels where it becomes energetically favorable for the membrane to shift to a state of enhanced permeability. If the membrane remains permeabilized long enough to disrupt homeostasis, cells eventually die. By utilizing this phenomenon, irreversible electroporation has had success in killing cancer cells and treating localized tumors. Additionally, if the pulse parameters are chosen to limit Joule heating, irreversible electroporation can be performed safely on surgically inoperable tumors located next to major blood vessels and nerves. As with all technologies, there is room for improvement. One drawback associated with therapeutic irreversible electroporation is that patients must be temporarily paralyzed and maintained under general anesthesia to prevent intense muscle contractions occurring in response to pulsing. The muscle contractions may be painful and can dislodge the electrodes. To overcome this limitation, we have developed a system capable of achieving non-thermal
A differentially regulated AP2/ERF transcription factor gene cluster acts downstream of a MAP kinase cascade to modulate terpenoid indole alkaloid biosynthesis in Catharanthus roseus.

Catharanthus roseus produces bioactive terpenoid indole alkaloids (TIAs), including the chemotherapeutics, vincristine and vinblastine. Transcriptional regulation of TIA biosynthesis is not fully understood. The jasmonic acid (JA)-responsive AP2/ERF transcription factor (TF), ORCA3, and its regulator, CrMYC2, play key roles in TIA biosynthesis. ORCA3 forms a physical cluster with two uncharacterized AP2/ERFs, ORCA4 and 5. Here, we report that (1) the ORCA gene cluster is differentially regulated; (2) ORCA4, while overlapping functionally with ORCA3, modulates an additional set of TIA genes. Unlike ORCA3, ORCA4 overexpression resulted in dramatic increase of TIA accumulation in C. roseus hairy roots. In addition, CrMYC2 is capable of activating ORCA3 and co-regulating TIA pathway genes concomitantly with ORCA3. The ORCA gene cluster and CrMYC2 act downstream of a MAP kinase cascade that includes a previously uncharacterized MAP kinase kinase, CrMAPKK1. Overexpression of CrMAPKK1 in C. roseus hairy roots upregulated TIA pathways genes and increased TIA accumulation. This work provides detailed characterization of a TF gene cluster and advances our understanding of the transcriptional and post-translational regulatory mechanisms that govern TIA biosynthesis in C. roseus.
Uttering: social micro-blogging without the internet

This paper studies a new potential social communication phenomenon: social micro-blogging without the Internet. Social micro-blogs (called utterances) are assumed created on mobile devices and shared between peers using direct wireless transmission rather than using any network infrastructure. This combines two emerging issues: opportunistic networking architectures are making it possible to "store, carry and forward" such content while trends in social media and self expression such as micro-blogging have become increasingly popular. We address the problem of obtaining content of personal interest through social micro-blogging without the Internet. This is a challenging problem because generally speaking, content cannot be pulled from its source on demand. Consequently intelligent techniques are needed that allow content to be pushed between groups of users. We introduce a community-based approach that allows content to be pushed to those who can derive utility from it. We explore the robustness and performance of this approach which builds social networks through which relevant content can be pushed using epidemic-inspired mechanisms.
CS for All: Catering to Diversity of Master's Students through Assignment Choices

Increasingly, students enrolled into foundational CS courses such as programming fundamentals include those from many non-CS majors including Data Analytics, Business, Science and Social Sciences. Staff teaching foundational programming courses must therefore cater for varying student backgrounds, cognitive abilities and interests while teaching abstract concepts such as encapsulation, inheritance and polymorphism. In the past assignments played a major role in learning such abstract concepts as they allowed students to construct their own meanings experientially. However, a single assignment in a given domain pitched at an average student cannot cater effectively to students with varying cognitive abilities and backgrounds resulting in poor learning outcomes and student satisfaction. In this paper we report our experience, substantially improving learning outcomes and student satisfaction in a Master's level introductory programming course with weak learning outcomes and poor student satisfaction by offering a choice of assignments. Our novel approach requires designing assignments which take into account the interests of students and their zone of proximal development which determines the extent to which a learner can grasp new concepts. Our pre and post assignment tests and survey feedback clearly show a substantial improvement in learning outcomes and student perception.
TiO2-Based Nanoheterostructures for Promoting Gas Sensitivity Performance: Designs, Developments, and Prospects

Gas sensors based on titanium dioxide (TiO2) have attracted much public attention during the past decades due to their excellent potential for applications in environmental pollution remediation, transportation industries, personal safety, biology, and medicine. Numerous efforts have therefore been devoted to improving the sensing performance of TiO2. In those effects, the construct of nanoheterostructures is a promising tactic in gas sensing modification, which shows superior sensing performance to that of the single component-based sensors. In this review, we briefly summarize and highlight the development of TiO2-based heterostructure gas sensing materials with diverse models, including semiconductor/semiconductor nanoheterostructures, noble metal/semiconductor nanoheterostructures, carbon-group-materials/semiconductor nano- heterostructures, and organic/inorganic nanoheterostructures, which have been investigated for effective enhancement of gas sensing properties through the increase of sensitivity, selectivity, and stability, decrease of optimal work temperature and response/recovery time, and minimization of detectable levels.
Protein structure model refinement in CASP12 using short and long molecular dynamics simulations in implicit solvent

Protein structure prediction has matured over years, particularly those which use structure templates for building a model. It can build a model with correct overall conformation in cases where appropriate templates are available. Models with the correct topology can be practically useful for limited purposes that need residue‐level accuracy, but further improvement of the models can allow the models to be used in tasks that need detailed structures, such as molecular replacement in X‐ray crystallography or structure‐based drug screening. Thus, model refinement is an important final step in protein structure prediction to bridge predictions to real‐life applications. Model refinement is one of the categories in recent rounds of critical assessment of techniques in protein structure prediction (CASP) and has recently been drawing more attention due to its realized importance. Here we report our group's performance in the refinement category in CASP12. Our method is based on inexpensive short molecular dynamics (MD) simulations in implicit solvent. Our performance in CASP12 was among the top, which was consistent with the previous round, CASP11. Our method with short MD runs achieved comparable performance with other methods that used longer simulations. Detailed analyses found that improvements typically occurred in entire regions of a structure rather than only in flexible loop regions. The remaining challenge in the structure refinement includes large conformational refinement which involves substantial motions of secondary structure elements or domains.
Altered DNA methylation in neonates born large-for-gestational-age is associated with cardiometabolic risk in children

Background Infants being born Large-for-gestational-age (LGA) are prone to developing cardiometabolic disease. However, the underlying mechanisms remain unclear. Results Clinical investigation showed that children born LGA had significantly higher serum level of total cholesterol (TC), low-density lipoprotein-cholesterol (LDL-c), and insulin, ratio of TC/high-density lipoprotein-cholesterol (HDL-c) compared to children born appropriate for gestational age (AGA). Birth weight (BW) was positively correlated to TC, LDL-c, and the ratio of TC/HDL in serum. Genome-wide DNA methylation analyzed in umbilical cord blood of controls and macrosomia cases. We identified 3459 methylation variable positions (MVPs) achieving genome-wide significance (adjusted P-value < 0.05) with methylation differences of ≥ 5%. A total of 327 MVPs were filtered by methylation differences of ≥ 7% located within an island, which mapped to 213 genes. Function analysis using Ingenuity Pathway Analysis showed 16 genes enriched in “cardiovascular disease”. Four genes included contributed to hyperlipidemia. Materials And Methods Fifty-eight children aged 3–6 years born LGA and 123 subjects born AGA were enrolled. Anthropometric parameters and blood pressure (BP) were measured, and metabolic assessment was performed in all subjects. Genome-wide DNA methylation in umbilical blood was assayed by the 450K BeadChip in six AGA and six macrosomia newborns. Conclusions Our data indicate that excess birth weight may increase the risk of lipid dysfunction in children aged 3–6 years. It might through reprogramming a group of genes correlated to cardiovascular disease. The genes identified in this study might be potential biomarker for cardiometabolic disease.