Miracle-dz/UniFAR-FTUs huggingface dataset:
The 8q24 Gene Desert: An Oasis of Non-Coding Transcriptional Activity

Understanding the functional effects of the wide-range of aberrant genetic characteristics associated with the human chromosome 8q24 region in cancer remains daunting due to the complexity of the locus. The most logical target for study remains the MYC proto-oncogene, a prominent resident of 8q24 that was first identified more than a quarter of a century ago. However, many of the amplifications, translocation breakpoints, and viral integration sites associated with 8q24 are often found throughout regions surrounding large expanses of the MYC locus that include other transcripts. In addition, chr.8q24 is host to a number of single nucleotide polymorphisms associated with cancer risk. Yet, the lack of a direct correlation between cancer risk alleles and MYC expression has also raised the possibility that MYC is not always the target of these genetic associations. The 8q24 region has been described as a “gene desert” because of the paucity of functionally annotated genes located within this region. Here we review the evidence for the role of other loci within the 8q24 region, most of which are non-coding transcripts, either in concert with MYC or independent of MYC, as possible candidate gene targets in malignancy.
Tfl deletion induces extraordinary Cxcl13 secretion and cachexia in VavP-Bcl2 transgenic mice

Statement of significance: Loss of TFL, found in several types of lymphoma, induces excessive CXCL13 secretion through RNA dysregulation contributing to body weight loss and early death in lymphoma model mice. Follicular lymphoma (FL) is associated with overexpressed BCL-2 and other genetic aberrations, including 6q-. We identified a novel gene on 6q25, “Transformed follicular lymphoma (TFL),” from a transformed FL. TFL regulates several cytokines via mRNA degradation, which has been suggested to underlie resolving inflammation. Fluorescence in situ hybridization revealed a deletion of TFL occurred in 13.6% of various B-cell lymphoma samples. We developed VavP-bcl2 transgenic, TFL deficit mice (Bcl2-Tg/Tfl -/-) to seek how TFL affects disease progression in this lymphoma model. While Bcl2-Tg mice developed lymphadenopathy and died around 50 weeks, Bcl2-Tg/Tfl -/- mice lost body weight around 30 weeks and died about 20 weeks earlier than Bcl2-Tg mice. Furthermore, we found a unique B220-IgM+ cell population in the bone marrow of Bcl2-Tg mice. cDNA array in this population revealed that Cxcl13 mRNA in Bcl2-Tg/Tfl -/- mice expressed significantly higher than Bcl2-Tg mice. In addition, bone marrow extracellular fluid and serum showed an extremely high Cxcl13 concentration in Bcl2-Tg/Tfl -/- mice. Among bone marrow cells, the B220-IgM+ fraction was the main producer of Cxcl13 in culture. A reporter assay demonstrated TFL regulates CXCL-13 via induction of 3’UTR mRNA degradation in B lineage cells. These data suggest Tfl regulates Cxcl13 in B220-IgM+ cells in the bone marrow, and a very high concentration of serum Cxcl13 arising from these cells may contribute to early death in lymphoma-bearing mice. Since several reports have suggested the association of CXCL13 expression with lymphoma, these findings provide new insights into cytokine regulation via TFL in lymphoma.
Patients’ Perspective on Participation in Care With or Without the Support of a Smartphone App During Radiotherapy for Prostate Cancer: Qualitative Study

Background Patients with prostate cancer are often cared for as outpatients during radiotherapy, which can be an aggravating circumstance for patient participation. There is a need to evaluate whether an interactive smartphone app could enable participation in care, specifically during treatment for prostate cancer. The interactive app (Interaktor) used in this study is developed in codesign with patients and health care professionals; it includes daily reports of symptoms, a risk assessment model, evidence-based self-care advice, along with the provision of immediate access to clinicians. Objective The aim of this study was to explore how patients with prostate cancer perceived their participation with or without the support of the smartphone app during radiotherapy. Methods A total of 28 prostate cancer patients receiving adjuvant radiotherapy were interviewed about their perceived participation in their own care. All the patients interviewed in this study participated in an intervention study where the control group received standard care that comprised having access to a contact nurse to turn to with any concerns during their treatment. In addition to standard care, the patients in the intervention group received the app downloaded in a smartphone. The patients’ age ranged between 57 and 77 years; 17 patients used the smartphone app. The interviews were analyzed with directed qualitative content analysis. Results The four dimensions of patient participation, which include mutual participation, fight for participation, requirement for participation, and participation in getting basic needs satisfied, were confirmed as valid perspectives in the interviews with the patients with prostate cancer, irrespective of whether they used the smartphone app. However, the patients who had used the smartphone app described it as a facilitating factor, especially for mutual participation. Conclusions Using innovative ways to communicate with patients, such as an interactive app for symptom management with contact with health care in real time, can successfully help achieve increased patient participation in care.
Dementia in Relation to Family Caregiver Involvement and Burden in Long-Term Care

To better understand the process and outcomes of family involvement for long-term care residents with varying stages of dementia, we analyzed family and staff data for 467 residents of 24 residential care/assisted living and nursing-home settings. Adjusted analyses found that although the amount of family visitation did not significantly vary by resident cognitive status (15 versus 20 visits/month to persons with and without dementia, respectively), the nature of the visit did. Families of cognitively intact residents spent more time in activities related to social and community engagement, such as taking residents on trips and calling and writing letters (p < .001), while families of more impaired residents spent more time on care-related activities, including tasks related to nutrition (p < .027), mobility (p = .001), and discussing care with staff (p = .007), the latter of which was associated with greater burden (p < .001). Staff identified similar patterns but perceived less family involvement.
Description and Optimization of Abstract Machines in a Dialect of Prolog*

Abstract In order to achieve competitive performance, abstract machines for Prolog and related languages end up being large and intricate, and incorporate sophisticated optimizations, both at the design and at the implementation levels. At the same time, efficiency considerations make it necessary to use low-level languages in their implementation. This makes them laborious to code, optimize, and, especially, maintain and extend. Writing the abstract machine (and ancillary code) in a higher-level language can help tame this inherent complexity. We show how the semantics of most basic components of an efficient virtual machine for Prolog can be described using (a variant of) Prolog. These descriptions are then compiled to C and assembled to build a complete bytecode emulator. Thanks to the high-level of the language used and its closeness to Prolog, the abstract machine description can be manipulated using standard Prolog compilation and optimization techniques with relative ease. We also show how, by applying program transformations selectively, we obtain abstract machine implementations whose performance can match and even exceed that of state-of-the-art, highly-tuned, hand-crafted emulators.
Effective Photoimmunotherapy of Murine Colon Carcinoma Induced by the Combination of Photodynamic Therapy and Dendritic Cells

Purpose: The unique mechanism of tumor destruction by photodynamic therapy (PDT), resulting from apoptotic and necrotic killing of tumor cells accompanied by local inflammatory reaction and induction of heat shock proteins (HSPs), prompted us to investigate the antitumor effectiveness of the combination of PDT with administration of immature dendritic cells (DCs). Experimental Design: Confocal microscopy and Western blotting were used to investigate the influence of PDT on the induction of apoptosis and expression of HSP expression in C-26 cells. Confocal microscopy and flow cytometry studies were used to examine phagocytosis of PDT-treated C-26 cells by DCs. Secretion of interleukin (IL)-12 was measured with ELISA. Cytotoxic activity of lymph node cells was evaluated in a standard 51Cr-release assay. The antitumor effectiveness of PDT in combination with administration of DCs was investigated in in vivo model. Results: PDT treatment resulted in the induction of apoptotic and necrotic cell death and expression of HSP27, HSP60, HSP72/73, HSP90, HO-1, and GRP78 in C-26 cells. Immature DCs cocultured with PDT-treated C-26 cells efficiently engulfed killed tumor cells, acquired functional features of maturation, and produced substantial amounts of IL-12. Inoculation of immature DCs into the PDT-treated tumors resulted in effective homing to regional and peripheral lymph nodes and stimulation of cytotoxic activity of T and natural killer cells. The combination treatment with PDT and administration of DCs produced effective antitumor response. Conclusions: The feasibility and antitumor effectiveness demonstrated in these studies suggest that treatment protocols involving the administration of immature DCs in combination with PDT may have clinical potential.
Science and Gamification: The Odd Couple?

This work-in-progress paper describes initial efforts to examine two opposite cases of citizen science projects, namely Galaxy Zoo and Foldit. Early findings from two case studies suggest that the use of gamification in these citizen science projects is contested. Statements from participants indicate that Foldit and Galaxy Zoo seem to fall, respectively, on the two dimensions of ludus and paidia, the former being rule-based and goal-oriented, and the latter being more oriented towards "playful experiences" in which participants can tap into motivations like curiosity and desire to learn.
Hyperventilation syndrome in adolescents with and without asthma

Data on the prevalence of hyperventilation syndrome (HVS) in adolescents are scanty. Objectives: To determine the prevalence of HVS in a population of adolescents with and without asthma, and to verify whether HVS was related to asthma activity. Methods: A population of adolescents was asked to self‐complete a questionnaire, including the Nijmegen questionnaire to assess HVS, and a standardized asthma questionnaire. Results: Seven hundred and sixty questionnaires were suitable for analysis. One hundred and twenty subjects (15.8%) were classified as asthmatic. Forty‐seven subjects (6.2%) had a Nijmegen score ≥23, which was suggestive of HVS. Symptoms indicative of HVS were ten times more common in subjects with asthma (25%) than in those without asthma (2.5%). Nijmegen score was significantly higher in subjects with lifetime asthma (P < 0.001), current episodic asthma (P < 0.05) and current active asthma (P < 0.001) than in those with no asthma. In the whole population, girls presented HVS more frequently than boys (P < 0.001). There was a significant effect of gender (females, OR 3.2) and status of asthma (lifetime asthma, OR 11.2; current episodic asthma, OR 8.9; current active asthma, OR 41.5) on the probability of suffering from HVS. Conclusions: The prevalence of symptoms indicative of HVS in an unselected population of adolescents was relatively high. Symptoms were more common in girls and in subjects with asthma, and there was a significant effect of asthma activity on the probability of suffering from HVS. Further studies need to be performed in order to validate a screening tool for HVS in both adolescents and asthmatic subjects. Pediatr Pulmonol. 2015; 50:1184–1190. © 2014 Wiley Periodicals, Inc.
Guidelines for carotid endarterectomy: a statement for healthcare professionals from a special writing group of the Stroke Council, American Heart Association.

Since the 1950s carotid endarterectomy has been performed in patients with symptomatic carotid artery stenosis, based on suggestive but inconclusive evidence for its effectiveness. Only during the last 5 years have randomized studies clarified the indications for surgery. In preparing this report, panel members used the same rules of evidence used in the previous report1 2 (Table⇓). View this table: Table 1. Levels of Evidence and Grading of Recommendations Few studies have analyzed control of risk factors in a randomized, prospective manner following carotid endarterectomy. However, a wealth of data are available regarding the general relationship between risk factor control and stroke risk. These data provide some guidance for the care of endarterectomy patients. ### Hypertension Hypertension is the most powerful, prevalent, and treatable risk factor for stroke.3 Both systolic and diastolic blood pressure are independently related to stroke incidence. Isolated systolic hypertension, which is common in the elderly, also considerably increases risk of stroke. Reduction of elevated blood pressure significantly lowers risk of stroke. Meta-analyses of randomized trials found that an average reduction in diastolic blood pressure of 6 mm Hg produces a 42% reduction in stroke incidence.3 4 Treatment of isolated systolic hypertension in people older than 60 years also reduces stroke incidence by 36% without an excessive number of side effects such as depression or dementia.5 Long-term care of patients after endarterectomy should include careful control of hypertension (Grade A recommendation for treatment of hypertension in general; Grade C recommendation for postendarterectomy care). Perioperative treatment of hypertension after carotid endarterectomy represents a special situation. Poor control of blood pressure after endarterectomy increases risk of cerebral hyperperfusion syndrome.6 7 8 9 This complication is characterized by unilateral headache, seizures, and occasionally altered mental status or focal neurological signs. Neuroimaging may show intracerebral hemorrhages10 11 12 or white …
Identification and characterization of KpsS, a novel polysaccharide sulphotransferase in Mesorhizobium loti

Plants enter into symbiotic relationships with bacteria that allow survival in nutrient‐limiting environments. The bacterium Mesorhizobium loti enters into a symbiosis with the legume host, Lotus japonicus, which results in the formation of novel plant structures called root nodules. The bacteria colonize the nodules, and are internalized into the cytoplasm of the plant cells, where they reduce molecular dinitrogen for the plant. Symbiosis between M. loti and L. japonicus requires bacterial synthesis of secreted and cell‐surface polysaccharides. We previously reported the identification of an unusual sulphate‐modified form of capsular polysaccharide (KPS) in M. loti. To better understand the physiological function of sulphated KPS, we isolated the sulphotransferase responsible for KPS sulphation from M. loti extracts, determined its amino acid sequence and identified the corresponding M. loti open reading frame, mll7563 (which we have named kpsS). We demonstrated that partially purified KpsS functions as a fucosyl sulphotransferase in vitro. Furthermore, mutants deficient for this gene exhibit a lack of KPS sulphation and a decreased rate of nodule formation on L. japonicus. Interestingly, the kpsS gene product shares no significant amino acid similarity with previously identified sulphotransferases, but exhibited sequence identity to open reading frames of unknown function in diverse bacteria that interact with eukaryotes.
Short Answer Grading: When Sorting Helps and When it Doesn’t

Automatic short-answer grading promises improved student feedback at reduced teacher effort both during and after instruction. Automated grading is, however, controversial in high-stakes testing and complex systems can be difficult to set up by non-experts, especially for frequently changing questions. We propose a versatile, domain-independent system that assists manual grading by pre-sorting answers according to their similarity to a reference answer. We show near state-ofthe-art performance on the task of automatically grading the answers from CREG (Meurers et al., 2011). To evaluate the grader assistance task, we present CSSAG (Computer Science Short Answers in German), a new corpus of German computer science questions answered by natives and highly-proficient non-natives. On this corpus, we demonstrate the positive influence of answer sorting on the slowest-graded, most complex-to-assess questions.
Lawnmower: Designing a web-based visual programming environment that generates code to help students learn textual programming

Learning programming can be a challenging task for design students, especially when code is to be entered in textual form. Visual programming languages, such as McNeil’s Grasshopper, have helped students to engage in scripting without having to deal with lower level syntax that is often hindering them in expressing their thoughts. However, the problem with learning how to program textually is only postponed: When switching to a new platform, students may be forced to learn coding from scratch, and, even worse, to do so in a textual environment that is yet unfamiliar. Our idea is simple: Connect visual programming with textual coding, using code-generation as means. Using this approach enables students to think visually, and see the results textually. An added bonus is the possibility to use debugging, a feature that is yet lacking from Grasshopper. By this way, our language aims to enable students to gradually move from visual to textual programming in a comfortable manner.
Implantation of a Multifocal Toric Intraocular Lens after Radial Keratotomy and Cross-Linking with Hyperopia and Astigmatism Residues: A Case Report

Radial keratotomy is a refractive surgical technique, widely used in the 80s and early 90s to correct myopia and astigmatism, but now overcome by more recent laser techniques. Important consequences, often in patients with more than 45 years of age, are progressive hyperopic shift and/or an increase in corneal astigmatism, whose main cause seems to be an increase in the curvature radius of the central portion of the cornea. This seems to be due to radial keratotomy incisions – with the consequent need for cross-linking – intraocular pressure, and corneal biomechanical parameters. The authors propose phacoemulsification with a customized multifocal toric intraocular lens implantation to correct the induced shift and hyperopic astigmatism. A decent postoperative visual acuity was observed with good patient satisfaction. A specific protocol must be applied to optimize the correct diagnosis, presurgical evaluation and postsurgical outcomes that are to be maintained over time, without regressions.
Shortened preanesthetic fasting interval in pediatric cardiac surgical patients.

The recent liberalization of preoperative feeding orders in healthy pediatric outpatients prompts the question of whether this applies to children about to have cardiac surgery. The authors compared gastric fluid volume and pH in two groups of children undergoing elective cardiac surgery, one of which was not only permitted ad libitum clear liquids but was mandated to drink clear liquids 2-3 h before induction of anesthesia (study group). The other group followed routine inpatient preoperative fasting orders (control group). The study group (n = 44) averaged 3.1 +/- 4.1 yr and weighed 15.3 +/- 16.3 kg; the control group averaged 3.3 +/- 3.9 yr and weighed 14.3 +/- 12.1 kg (P = 0.82, 0.73, respectively). Aspiration of residual gastric fluid volume was attempted in all patients after induction of anesthesia. Gastric fluid volume averaged 0.6 +/- 0.9 mL/kg in the study group and 0.4 +/- 0.6 mL/kg in the control group (P = 0.13). Of the study patients, 41% had a measured gastric volume greater than or equal to 0.4 mL/kg compared with 32% of the control patients (P = 0.50). Of the 42 patients who had residual gastric fluid aspirated, pH determinations were completed on 37 aspirates; of these 19 of 20 (95%) in the study group and 14 of 17 (82%) in the control group had a gastric pH less than or equal to 2.5. Using a linear analogue scale, parents rated children in the study group to be more comfortable, less hungry, and less thirsty compared with the control patients (P = 0.004, 0.002, 0.0001, respectively). (ABSTRACT TRUNCATED AT 250 WORDS)
280GHz and 860GHz image sensors using Schottky-barrier diodes in 0.13μm digital CMOS

Millimeter and sub-millimeter-wave imaging using solid-state circuits is gaining attention for security and medical applications. To lower cost and increase integration, MOSFETs in CMOS are being investigated for implementing broadband detectors [1-3]. However, neither measured noise-equivalent power (NEP) nor noise floor of the imager was given in [1]. Although NEP of 17pW/Hz1/2 was achieved at 650GHz in [2], an external lens was attached to the 65nm SOI CMOS chip. In [3], an NEP of 66pW/Hz1/2 was measured at 1.05THz using 65nm CMOS without a lens attached to the chip. Additionally, although the efforts reported in [1-3] realized an array, none demonstrated the image-array function. As an alternative, polysilicon-gate-separation (PGS) Schottky-barrier diodes (SBD) with cut-off frequency of ~2THz were fabricated in CMOS without process modifications [4] and were used to demonstrate a 280GHz detector with NEP of 30pW/Hz1/2 [5,6]. To significantly enhance the scanning speed, a 16-pixel 280GHz SBD imager is fabricated and its array function is reported in this paper. The imager including baseband amplifiers achieves responsivity of 5.1kV/W and NEP of 29pW/Hz1/2. More importantly, its operation was demonstrated in a setup that requires no mirror or lens that is bulky and costly. Next, an 860GHz SBD detector is demonstrated with a measured non-amplified responsivity of 355V/W and NEP of 32pW/Hz1/2. This NEP is ~2X lower than the best reported work in CMOS [3]. Both chips are fabricated in a 0. 13μm logic CMOS. The results suggest a path for high performance, compact and affordable sub-millimeter-wave and terahertz CMOS imagers using SBDs.
“I will change the world”: The Intersection of Social Change and Male College Athletes’ Leadership Perspectives

Historically, men have been characterized as task-oriented leaders who are motivated by desires for autonomy, wealth, and power (17, 33). However, these “masculine” views of leadership might not accurately capture the leadership motivations of Millennial males as the views were developed in previous generations (4). Given the commitment of many Millennials towards socially responsible attitudes and behaviors (18, 25), we utilized a qualitative research design to examine the influence of social change on the leadership motivations of Millennial male intercollegiate athletes. In doing so, we found participants were motivated to lead in order to affect social change within their communities and within society. Our findings indicate a new perspective, one which includes a commitment to social change, is potentially needed when discussing “masculine” views of leadership.