Miracle-dz/UniFAR-FTUs huggingface dataset:
FixL of Rhizobium meliloti enhances the transcriptional activity of a mutant FixJD54N protein by phosphorylation of an alternate residue

In Rhizobium meliloti, transcription of nitrogen fixation genes is induced in oxygen-depleted conditions under the control of the two-component regulatory system FixLJ. FixJ is a transcriptional activator whose activity is dramatically enhanced by phosphorylation, whereas FixL is a hemoprotein kinase that controls the level of phosphorylated FixJ in response to oxygen availability. We have found that a mutant FixJ protein, FixJD54N, in which the presumed site of phosphorylation (aspartate 54) was changed to an asparagine, is strongly affected for phosphorylation by FixL and is not detectably phosphorylated from the low-molecular-weight phosphate donor, acetyl-phosphate. Unexpectedly, FixL strongly enhances the transcriptional activity of the FixJD54N protein both in vivo and in vitro. We present evidence that FixJD54N transcriptional activity is enhanced by phosphorylation of an alternate residue in a reaction that requires FixL and ATP and is not affected by oxygen. We also demonstrate the key role of Asp-54 of FixJ in oxygen signal transduction.
The Focusing Manner Scale: its validity, research background and its potential as a measure of embodied experiencing

Focusing is an embodied practice where one attends to a bodily felt sense and uses it in understanding the self and situations. Several focusing professionals have referred to what they call “focusing attitudes” and speculated that incorporating these attitudes enhanced the practice of focusing and psychotherapy. In Japan, Fukumori and Morikawa developed the Focusing Manner Scale (FMS), a scale to measure the degree to which one has focusing attitudes. Since then, many studies utilizing FMS have shown positive correlations or causal relationships between focusing attitudes and holistic wellbeing. The objective of this paper is twofold. The first objective is to inform the English-speaking world about FMS and its research studies. An English version of the FMS (FMS-A.E) is presented in this paper. The second objective is to examine if long-term focusing practice leads to enhanced FMS scores. This examination also sheds light on the construct validity of FMS. A comparison of focusing professionals and people who have had no focusing experience showed that focusing professionals showed significantly higher scores on all subscales of the FMS.
Analysis of user comments: An approach for software requirements evolution

User feedback is imperative in improving software quality. In this paper, we explore the rich set of user feedback available for third party mobile applications as a way to extract new/changed requirements for next versions. A potential problem using this data is its volume and the time commitment involved in extracting new/changed requirements. Our goal is to alleviate part of the process through automatic topic extraction. We process user comments to extract the main topics mentioned as well as some sentences representative of those topics. This information can be useful for requirements engineers to revise the requirements for next releases. Our approach relies on adapting information retrieval techniques including topic modeling and evaluating them on different publicly available data sets. Results show that the automatically extracted topics match the manually extracted ones, while also significantly decreasing the manual effort.
Probiotics Reduce the Risk of Necrotizing Enterocolitis in Preterm Infants: A Meta-Analysis

Background: Necrotizing enterocolitis (NEC) is the most common serious acquired disease of the gastrointestinal tract in preterm infants. Probiotic bacteria are live microbial supplements that colonize the gastrointestinal tract and potentially provide benefit to the host. Objective: To compare the efficacy and safety of prophylactic enteral probiotics administration versus placebo or no treatment in the prevention of severe NEC and other morbidities in preterm infants. Methods: A meta-analysis was performed in accordance with the Cochrane Neonatal Review Group methods. Preterm infants <37 weeks’ gestational age and/or <2,500 g birth weight were included. Literature searches were made of MEDLINE, EMBASE, Cochrane Library Controlled Trials Register (CENTRAL), and abstracts of annual meetings of the Society for Pediatric Research and the European Society of Pediatric Research. Results: Nine eligible trials randomizing 1,425 infants were included. Included trials were highly variable with regard to enrollment criteria, baseline risk of NEC in the control groups, timing, dose, formulation of the probiotics, and feeding regimens. In a meta-analysis, enteral probiotics supplementation significantly reduced the incidence of severe NEC [typical RR 0.32 (95% CI 0.17, 0.60)] and mortality [typical RR 0.43 (95% CI 0.25, 0.75)]. There was no evidence of significant reduction of nosocomial sepsis [typical RR 0.93 (95% CI 0.73, 1.19)] or days on total parenteral nutrition [weighted mean difference –1.9 (95% CI –4.6, 0.77)]. The statistical test of heterogeneity for NEC, mortality and sepsis was insignificant. Data regarding extremely low birth weight infants (ELBW) could not be extrapolated. The included trials reported no systemic infection with the probiotics supplemental organism. Conclusion: Enteral supplementation of probiotics reduces the risk of severe NEC and mortality in preterm infants. A large randomized controlled trial is required to investigate the benefit and safety profile of probiotics supplementation in ELBW infants.
Rendering Visible the Invisible: Police Discretion, Professionalism and Decision-making

That police officers operate with considerable discretion is a staple of criminological literature. Based on an observational study of a British police service, this article explores the impact of a positive arrest policy that considerably reduced the extent to which officers could use their discretion when dealing with incidents of domestic violence. The basis of the policy was that the police service should treat this type of crime more seriously than has often been the case, and that the tendency for such crimes to escalate in their gravity means that an early intervention offers a more effective means of risk management. The article explores the reasons why officers tended to find the limits that this policy placed on their discretion difficult to reconcile with their notion of their own professionalism, and suggests that it raises difficult questions about ethical policing and victim-centred approaches.
Landscape change in the lower Omo valley, southwestern Ethiopia: burning patterns and woody encroachment in the savanna

Abstract In this article we examine bush encroachment in a savanna ecosystem of the lower Omo Valley occupied by Mursi agro-pastoralists. Focusing on the role of fire and grazing, the main anthropogenic disturbance factors in the savanna, we compare the results of our ecological surveys with Mursi perceptions and understandings of environmental change. The main change described by Mursi is the loss of grassland over the last 30 to 40 years. Their explanations centre on three complementary factors: a growth in human and livestock numbers, leading to a reduction in grass availability; a tendency towards more permanent settlement, leading to heavy year-round pressure on certain grazing areas; and the loss of traditional burning practices, leading to frequent small fires rather than infrequent large blazes, capable of clearing the savanna of trees. In addition, state encroachment in general and the establishment of the Omo and Mago National Parks in particular have restricted mobility and reduced the actual and potential grazing area available to Mursi livestock. Our ecological surveys did not, however, show a causal relationship between fire, grazing and encroachment pattern. We therefore suggest that grazing and burning practices should be considered relevant, but not necessarily the most important, factors explaining bush encroachment in this case.
Learning From the News in Campaign 2000: An Experimental Comparison of TV News, Newspapers, and Online News

The present study seeks to contribute to the literature on learning differences across media by extending the traditional television news versus newspaper comparison to include reading of online news. It employs an experimental design, but with exposure over time and a reasonable delay between exposure and the measurement of learning. It also moves beyond simple comparisons of effects to examine potential information-processing explanations for any differences that may appear across conditions as the result of both experimental demand and real differences across media. The results suggest that the medium of communication may have different effects depending on the type of learning measured. Recall of news stories tended to favor television and print newspapers compared to online newspapers, but structuring of election knowledge favored online newspapers compared to print and television news. In addition, findings suggest that information-processing behaviors-specifically attention-are encouraged by a combination of the nature of the medium and the experimental context.
Hegel on Legal and Moral Responsibility

When Hegel first addresses moral responsibility in the Philosophy of Right, he presupposes that agents are only responsible for what they intended to do, but appears to offer little, if any, justification for this assumption. In this essay, I claim that the first part of the Philosophy of Right, “Abstract Right”, contains an implicit argument that legal or external responsibility (blame for what we have done) is conceptually dependent on moral responsibility proper (blame for what we have intended). This overlooked argument satisfies the first half of a thesis Hegel applies to action in the Encyclopaedia Logic, namely, that the outer must be inner, and thus provides a necessary complement for his more explicit treatment of the second half of that thesis, that the inner must be outer. The claim that agents are only responsible for what they intended to do might appear, at first, to risk conflating legal and moral responsibility and to lack the necessary means to deal with the phenomenon of moral luck, but I argue that if it is properly situated within the whole of Hegel's philosophy of action it can be saved from both of these consequences and so take its place as an essential component of Hegel's full theory of moral responsibility.
Corticotropin-Releasing Factor Increases GABA Synaptic Activity and Induces Inward Current in 5-Hydroxytryptamine Dorsal Raphe Neurons

Stress-related psychiatric disorders such as anxiety and depression involve dysfunction of the serotonin [5-hydroxytryptamine (5-HT)] system. Previous studies have found that the stress neurohormone corticotropin-releasing factor (CRF) inhibits 5-HT neurons in the dorsal raphe nucleus (DRN) in vivo. The goals of the present study were to characterize the CRF receptor subtypes (CRF-R1 and -R2) and cellular mechanisms underlying CRF–5-HT interactions. Visualized whole-cell patch-clamp recording techniques in brain slices were used to measure spontaneous or evoked GABA synaptic activity in DRN neurons of rats and CRF effects on these measures. CRF-R1 and -R2-selective agonists were bath applied alone or in combination with receptor-selective antagonists. CRF increased presynaptic GABA release selectively onto 5-HT neurons, an effect mediated by the CRF-R1 receptor. CRF increased postsynaptic GABA receptor sensitivity selectively in 5-HT neurons, an effect to which both receptor subtypes contributed. CRF also had direct effects on DRN neurons, eliciting an inward current in 5-HT neurons mediated by the CRF-R2 receptor and in non-5-HT neurons mediated by the CRF-R1 receptor. These results indicate that CRF has direct membrane effects on 5-HT DRN neurons as well as indirect effects on GABAergic synaptic transmission that are mediated by distinct receptor subtypes. The inhibition of 5-HT DRN neurons by CRF in vivo may therefore be primarily an indirect effect via stimulation of inhibitory GABA synaptic transmission. These results regarding the cellular mechanisms underlying the complex interaction between CRF, 5-HT, and GABA systems could contribute to the development of novel treatments for stress-related psychiatric disorders.
Concurrent chemoradiotherapy degrades the quality of life of patients with stage II nasopharyngeal carcinoma as compared to radiotherapy

The purpose of this study was to compare the quality of life (QoL) of stage II nasopharyngeal carcinoma (NPC) patients treated with radiotherapy (RT) versus concurrent chemoradiotherapy (CCRT). In a cross-sectional study, these patients were treated with RT (n = 55) or CCRT (n = 51) between June 2008 and June 2013. For all subjects, disease-free survival was more than 3 years. QoL was assessed using the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire-Core 30 (EORTC QLQ-C30) questions and the Head and Neck 35 (EORTC QLQ-H&N35) questions. RT had better outcomes than CCRT for global QoL, functional scales, symptom scales of fatigue and insomnia, financial problems, and weight gain. Survivors receiving 1 cycle of concurrent chemotherapy had worse QoL outcomes than survivors receiving 2 cycles of concurrent chemotherapy. Patients receiving 3 cycles of concurrent chemotherapy had the best QoL outcomes. Thus, CCRT adversely affects the QoL of patients with stage II NPC as compared to radiotherapy.
Preoperative Chemoradiation in Locally Advanced Rectal Cancer: Efficacy and Safety

Background Preoperative chemoradiation (CRT) is considered the standard of care in the management of stage II/III rectal cancer. The aim of this retrospective study was to assess the efficacy and safety of preoperative CRT in our patient cohort with locally advanced rectal adenocarcinoma. Methods Forty patients with cT3-4N0-2M0 adenocarcinoma of the lower (n = 26) and mid/upper (n = 14) rectum were enrolled in this study between 2001 and 2012. Radiotherapy (RT) was given to the pelvis. The median prescribed dose was 45 Gy (daily dose, 1.8 - 2.0 Gy). All patients received chemotherapy concurrently with RT and underwent surgery 6 - 8 weeks after CRT. Low anterior resection (LAR) was achieved in 21 patients. Total mesorectal excision (TME) was performed in 24 patients. Results Tumor downstaging (expressed as TN downstaging) was observed in 15 patients (38%); a pathological complete response (pCR) was pathologically confirmed in six of them. In nine out of the 26 (23%) patients with low lying tumors, sphincter preservation (SP) was possible. SP was also possible in all but one patient (13%) who achieved a pCR. In three out of 15 patients (8%) with preoperative sphincter infiltration, SP was achieved. With a median follow-up of 58 months, the 4-year local control (LC), distant metastases-free survival (DMFS), disease-free survival (DFS) and overall survival (OS) rates were 89.7%, 86.9%, 79.5% and 81.2%, respectively. The pretreatment tumor size was predictive of response to preoperative CRT. The response to preoperative CRT did show a significant impact on DFS and on OS. TME resulted in a statistically significant increased DFS rate. No grade 3/4 acute toxicity was reported. Three patients developed grade 3 late side effects. Conclusion Preoperative CRT demonstrates encouraging rates of disease control and facilitates complete resection and SP in advanced rectal cancer with acceptable late toxicity.
The nuclear transcription factor kappaB/bcl-2 pathway correlates with pathologic complete response to doxorubicin-based neoadjuvant chemotherapy in human breast cancer.

PURPOSE Molecular factors involved in apoptosis may affect breast cancer response to chemotherapy. Herein, we studied the nuclear factor kappaB (NF-kappaB)/bcl-2 pathway to determine whether or not activation of this antiapoptotic pathway was associated with a poor response of human breast cancer to anthracycline-based neoadjuvant chemotherapy. EXPERIMENTAL DESIGN We studied 82 human breast cancer samples from patients treated with neoadjuvant doxorubicin-based chemotherapy and studied whether or not nuclear location of the transcription factor NF-kappaB was associated with expression of bcl-2 and bax and whether or not expression of these proteins correlated with chemotherapy response. Protein expression was measured with immunohistochemical staining. A dedicated breast cancer pathologist who was unaware of the clinical outcome data dichotomized the slides as positive or negative based on the presence or absence of cytoplasmic staining for bcl-2 and bax or nuclear staining for NF-kappaB. RESULTS Sixty-one percent of the tumors were positive for bcl-2, 85% were positive for bax, and 16% were positive for NF-kappaB. All bcl-2-positive tumors were also bax positive (P < 0.0001) and all NF-kappaB-positive tumors were both bcl-2 positive (P = 0.001) and bax positive (P = 0.113). Eleven of the 82 patients (13%) had a pathologic complete response (pCR) to chemotherapy. Patients with positive staining tumors for any of the markers less commonly achieved a pCR to chemotherapy than those with negative tumor staining. The pCR rates were NF-kappaB positive 0% (0 of 13) versus NF-kappaB negative 13% (11 of 69; P = 0.130); bcl-2 positive 4% (2 of 49) versus bcl-2 negative 27% (9 of 33; P = 0.004); and bax positive 6% (4 of 69) versus bax negative 58% (7 of 12; P < 0.001). CONCLUSION We conclude that nuclear localization of NF-kappaB correlates with bcl-2 and bax expression and that the NF-kappaB/bcl-2 pathway may be associated with a poor response to neoadjuvant doxorubicin-based chemotherapy.
Back to School: An Examination of the Evening University and the Caribbean's Nontraditional Student

Abstract The Evening University (EU) programme at the University of the West Indies offers an opportunity for working adults and nontraditional students to earn undergraduate degrees. A qualitative framework was used to explore the reasons those enrolled in this programme sought tertiary education and to identify any challenges they faced throughout their tertiary career. Two focus group interviews were conducted with 16 participants who were asked to discuss factors influencing their decision to enroll in the EU and the challenges faced while studying for their undergraduate degrees. Since this research also aimed to evaluate students’ opinions of the EU programme, participants were also asked to give their assessment of the programme. The findings revealed that students were motivated by intrinsic and extrinsic factors. Balancing study responsibilities with employment demands proved to be most challenging. Respondents expressed disappointment with their experience in the Evening University programme.
Cementation of Primary Aneurysmal Bone Cysts

The effects of polymethylmethacrylate (bone cement) on the local control of primary aneurysmal bone cysts excluding spinal lesions were analyzed. After intensive curettage of the lesions, 30 patients underwent a bone graft, and 35 patients had the defect packed with bone cement. After cementation(median time lapse, 4.5 months), 30 of 35 patients underwent a cancellous bone graft after removal of the packed bone cement. The followup period ranged between 24 and 161 months (median, 59.5 months). The local recurrence rate after curettage and cementation was 17% and after curettage and bone graft was 37%. The difference of the cumulative 10-year relapse free survival between patients of both groups was significant. The median time between surgery and local recurrence was 17 months (range, 2-90 months).
Mannan-Binding Lectin–Associated Serine Protease 1/3 Cleavage of Pro–Factor D into Factor D In Vivo and Attenuation of Collagen Antibody-Induced Arthritis through Their Targeted Inhibition by RNA Interference–Mediated Gene Silencing

The complement system is proposed to play an important role in the pathogenesis of rheumatoid arthritis (RA). The complement system mannan-binding lectin–associated serine proteases (MASP)-1/3 cleave pro–factor D (proDf; inactive) into Df (active), but it is unknown where this cleavage occurs and whether inhibition of MASP-1/3 is a relevant therapeutic strategy for RA. In the present study, we show that the cleavage of proDf into Df by MASP-1/3 can occur in the circulation and that inhibition of MASP-1/3 by gene silencing is sufficient to ameliorate collagen Ab–induced arthritis in mice. Specifically, to examine the cleavage of proDf into Df, MASP-1/3–producing Df−/− liver tissue (donor) was transplanted under the kidney capsule of MASP-1/3−/− (recipient) mice. Five weeks after the liver transplantation, cleaved Df was present in the circulation of MASP-1/3−/− mice. To determine the individual effects of MASP-1/3 and Df gene silencing on collagen Ab–induced arthritis, mice were injected with scrambled, MASP-1/3–targeted, or Df-targeted small interfering RNAs (siRNAs). The mRNA levels for MASP-1 and -3 decreased in the liver to 62 and 58%, respectively, in mice injected with MASP-1/3 siRNAs, and Df mRNA decreased to 53% in the adipose tissue of mice injected with Df siRNAs; additionally, circulating MASP-1/3 and Df protein levels were decreased. In mice injected with both siRNAs the clinical disease activity, histopathologic injury scores, C3 deposition, and synovial macrophage/neutrophil infiltration were significantly decreased. Thus, MASP-1/3 represent a new therapeutic target for the treatment of RA, likely through both direct effects on the lectin pathway and indirectly through the alternative pathway.
Comparing Shocks and Frictions in Us and Euro Area Business Cycles: A Bayesian DSGE Approach

This paper estimates a DSGE model with many types of shocks and frictions for both the US and the euro area economy over a common sample period (1974-2002). The structural estimation methodology allows us to investigate whether differences in business cycle behaviour are due to differences in the type of shocks that affect the two economies, differences in the propagation mechanism of those shocks or differences in the way the central bank responds to those economic developments. Our main conclusion is that each of those characteristics is remarkably similar across both currency areas.
Efficient Spectral-Galerkin Method I. Direct Solvers of Second- and Fourth-Order Equations Using Legendre Polynomials

This paper presents some efficient algorithms based on the Legendre–Galerkin approximations for the direct solution of the second- and fourth-order elliptic equations. The key to the efficiency of these algorithms is to construct appropriate base functions, which lead to systems with sparse matrices for the discrete variational formulations. The complexities of the algorithms are a small multiple of $N^{d + 1} $ operations for a d-dimensional domain with $(N - 1)^d $ unknowns, while the convergence rates of the algorithms are exponential for problems with smooth solutions. In addition, the algorithms can be effectively parallelized since the bottlenecks of the algorithms are matrix-matrix multiplications.