Miracle-dz/UniFAR-FTUs huggingface dataset:
Network Analysis Reveals a Role for Salicylic Acid Pathway Components in Shade Avoidance1[OPEN]

Shade avoidance involves complex regulation of multiple hormone network modules, and salicylic acid pathway genes are required for petiole shade avoidance. Plants have sophisticated mechanisms for sensing neighbor shade. To maximize their ability to compete for light, plants respond to shade through enhanced elongation and physiological changes. The shade avoidance response affects many different organs and growth stages, yet the signaling pathways underlying this response have mostly been studied in seedlings. We assayed transcriptome changes in response to shade across a 2-d time course in the wild type and 12 Arabidopsis (Arabidopsis thaliana) mutants. The resulting temporal map of transcriptional responses to shade defines early and late responses in adult plants, enabling us to determine connections between key signaling genes and downstream responses. We found a pervasive and unexpectedly strong connection between shade avoidance and genes related to salicylic acid, suggesting salicylic acid signaling to be an important shade avoidance growth regulator. We tested this connection and found that several mutants disrupting salicylic acid levels or signaling were defective in shade avoidance. The effect of these mutations on shade avoidance was specific to petiole elongation; neither hypocotyl nor flowering time responses were altered, thereby defining important stage-specific differences in the downstream shade avoidance signaling pathway. Shade treatment did not change salicylic acid levels, indicating that the mediation of shade avoidance by salicylic acid is not dependent on the modulation of salicylic acid levels. These results demonstrate that salicylic acid pathway genes also are key components of petiole shade avoidance.
Designing Welcoming and Inclusive STEM Department Websites

⎯ Websites have tremendous power to create first impressions. Prospective and current students and employees increasingly rely on the Internet for information about academic programs, people, and institutions. Department websites are one source for that information, but they also convey information about departmental culture and environment. Culturecommunication certainly derives from content, but just as importantly, it is impacted by design and structure. Engineering and science departments interested in broadening their appeal to underrepresented groups must look to their own websites. What culture is being communicated – explicitly, implicitly – and to whom does it appeal? The Kansas State University ADVANCE project team recognizes the power of website messages. Six K-State science and engineering departments have worked for two years on an ADVANCE-sponsored website initiative. These departments agreed to work on improving delivery of welcoming and inclusive messages to students, faculty, and staff via their departmental websites. They participated in a three-step process: workshops; revision of existing websites; evaluation and feedback. This paper shares information about each step of the process, the lessons learned, and best practices that have been identified. Introduction It is almost a given that the Internet has dramatically changed nearly every aspect of Western society. This is particularly true at universities, which were the original nodes on the Internet (History of Computing Project, 2001). University faculty members in science, technology, engineering, and mathematics (STEM) departments have incorporated Internet use into their teaching, research, and service, and, as the WorldWideWeb and web browsers became available, they developed websites to share information with and advertise themselves to a variety of constituents. However, unlike the case of for-profit companies, which came later to the web and made use of professional designers, many university-related websites, particularly those of individual academic departments and faculty members, were not professionally designed. Many academic department websites were developed by one or two enthusiastic faculty members or designed by students interested in web creation. As a result, the content and aesthetics of department websites vary widely. Students, particularly ‘Millennials’ who grew up with the Internet, now use it as their main source of information on many topics (Oblinger, 2003). Departments should be conscious of this fact and ensure that their websites convey the message that they wish since websites in many cases are their primary public faces. It is not enough for departments to simply place
Sleep quality, pain, anxiety, depression and quality of life in patients with frozen shoulder1.

BACKGROUND Nocturnal shoulder pain could play an essential role in frozen shoulder (FS) and can lead to disturbed sleep, anxiety, depression and reduced quality of life (QoL). OBJECTIVE The aim of this study was to examine anxiety, depression, sleep quality and quality of life in patients with FS and compare these to healthy controls. METHODS We prospectively evaluated 148 participants (76 FS patients and 72 healthy controls). We obtained Visual Analogue Scale (VAS) pain score, Beck Anxiety Inventory (BAI), Beck Depression Inventory (BDI), Pittsburgh Sleep Quality Index (PSQI) and World Health Organization Quality of Life Scale short form (WHOQoL-BREF). RESULTS FS patients had significantly higher scores for VAS and BAI (p< 0.001) than the control group. There was no significant difference between the BDI scores of the groups (p= 0.067). The WHOQoL-BREF scale of the physical, mental and environmental fields were significantly lower in the FS group (p< 0.001). FS patients had significantly lower sleep efficiency, and sleep disorders in terms of PSQI section scores (p< 0.001). CONCLUSION Our study demonstrated that there is a high prevalence and close relationships of pain, anxiety and sleep disturbance in patients with FS. Adding a psychiatric evaluation to the treatment of patients with FS may be beneficial.
The amino acid composition and protein quality of various egg, poultry meal by-products, and vegetable proteins used in the production of dog and cat diets

ABSTRACT New protein ingredients are used to support pet food market growth and the development of new products while maintaining animal dietary needs. However, novel protein sources (e.g., spray‐dried chicken, and (or) rice, pea, and potato protein concentrates) have limited data available regarding their protein quality. The objective of this study was to evaluate protein ingredients used in the pet food industry by laboratory analysis and a chick growth assay as a model. Following analysis for proximate and amino acid composition, chicks (six birds per pen with four pens per treatment) were fed experimental diets for 10 d. Diets contained 10% crude protein from each of the experimental protein sources (spray‐dried egg—SDEG; spray‐dried egg white—SDEW, spray‐dried inedible whole egg—SDIE, chicken by‐product meal—CBPM, chicken meal—CKML, low‐temperature fluid bed air‐dried chicken—LTCK, low‐temperature and pressure fluid bed dried chicken—LTPC, spray‐dried chicken—SDCK, whey protein concentrate—WPCT, corn gluten meal—CGML, corn protein concentrate—CPCT, potato protein isolate—PPIS, rice protein concentrate—RPCT, pea protein isolate—PEPI, soy protein isolate—SPIS, and soybean meal—SBML) along with an N‐free diet (negative control). Chicks fed SDEG, SDIE, and LTPC had the highest protein efficiency ratio (PER; P < 0.0001; 5.18, 5.37, and 5.33, respectively), LTCK and SDCK were intermediate (4.54 and 4.79), and the CBPM and CKML were the lowest among the poultry proteins for EAA:NEAA, PER, and Lys availability. Among the vegetable proteins, PPIS and SBML had the highest PER values (3.60 and 3.48, P < 0.0001). In general, the chick PER method ranked the quality of animal protein sources higher than vegetable proteins, and these results were consistent with the EAA:NEAA ratio and Lys availability.
Recommending Who to Follow in the Software Engineering Twitter Space

With the advent of social media, developers are increasingly using it in their software development activities. Twitter is one of the popular social mediums used by developers. A recent study by Singer et al. found that software developers use Twitter to “keep up with the fast-paced development landscape. ” Unfortunately, due to the general-purpose nature of Twitter, it’s challenging for developers to use Twitter for their development activities. Our survey with 36 developers who use Twitter in their development activities highlights that developers are interested in following specialized software gurus who share relevant technical tweets. To help developers perform this task, in this work we propose a recommendation system to identify specialized software gurus. Our approach first extracts different kinds of features that characterize a Twitter user and then employs a two-stage classification approach to generate a discriminative model, which can differentiate specialized software gurus in a particular domain from other Twitter users that generate domain-related tweets (aka domain-related Twitter users). We have investigated the effectiveness of our approach in finding specialized software gurus for four different domains (JavaScript, Android, Python, and Linux) on a dataset of 86,824 Twitter users who generate 5,517,878 tweets over 1 month. Our approach can differentiate specialized software experts from other domain-related Twitter users with an F-Measure of up to 0.820. Compared with existing Twitter domain expert recommendation approaches, our proposed approach can outperform their F-Measure by at least 7.63%.
Genotypic variation in phenological plasticity: Reciprocal common gardens reveal adaptive responses to warmer springs but not to fall frost

Species faced with rapidly shifting environments must be able to move, adapt, or acclimate in order to survive. One mechanism to meet this challenge is phenotypic plasticity: altering phenotype in response to environmental change. Here, we investigated the magnitude, direction, and consequences of changes in two key phenology traits (fall bud set and spring bud flush) in a widespread riparian tree species, Populus fremontii. Using replicated genotypes from 16 populations from throughout the species’ thermal range, and reciprocal common gardens at hot, warm, and cool sites, we identified four major findings: (a) There are significant genetic (G), environmental (E), and GxE components of variation for both traits across three common gardens; (b) The magnitude of phenotypic plasticity is correlated with provenance climate, where trees from hotter, southern populations exhibited up to four times greater plasticity compared to the northern, frost‐adapted populations; (c) Phenological mismatches are correlated with higher mortality as the transfer distances between provenance and garden increase; and (d) The relationship between plasticity and survival depends not only on the magnitude and direction of environmental transfer, but also on the type of environmental stress (i.e., heat or freezing), and how particular traits have evolved in response to that stress. Trees transferred to warmer climates generally showed small to moderate shifts in an adaptive direction, a hopeful result for climate change. Trees experiencing cooler climates exhibited large, non‐adaptive changes, suggesting smaller transfer distances for assisted migration. This study is especially important as it deconstructs trait responses to environmental cues that are rapidly changing (e.g., temperature and spring onset) and those that are fixed (photoperiod), and that vary across the species’ range. Understanding the magnitude and adaptive nature of phenotypic plasticity of multiple traits responding to multiple environmental cues is key to guiding restoration management decisions as climate continues to change.
Influence of thiopurine S‐methyltransferase polymorphisms in mercaptopurine pharmacokinetics in healthy volunteers

Mercaptopurine is a drug commonly used in the treatment of different types of cancer, especially acute lymphoblastic leukaemia, and autoimmune diseases such as ulcerative colitis or Crohn's disease and in patients receiving organ transplants. It is metabolized by three cytosolic enzymes. One of them, thiopurine S‐methyltransferase (TPMT), is responsible for catalysing the methylation reaction of mercaptopurine to 6‐methylmercaptopurine, thus inactivating the drug. Individuals with TPMT loss‐of‐function alleles (*2, *3A, *3B or *3C) can be extremely sensitive to the effect of mercaptopurine, since it can be accumulated, therefore producing haematological toxicity. The objective of this study was to evaluate the role of TPMT polymorphisms on the pharmacokinetics of mercaptopurine. For that purpose, we used collected pharmacokinetic data from 48 healthy volunteers (all males) who received a single oral dose of mercaptopurine 50 mg in two bioequivalence studies. The volunteers were subsequently genotyped for TPMT *2, *3A, *3B and *3C alleles by real‐time PCR. There were four carriers (8.3%) of TPMT*2 and TPMT*3A alleles. Mercaptopurine elimination was affected by TPMT loss‐of‐function polymorphisms, since heterozygous subjects show 18% higher half‐life compared to wild‐type individuals. This fact is consistent with the expected since the presence of loss‐of‐function alleles decreases TPMT enzymatic activity and, thus, affects mercaptopurine elimination. Moreover, mercaptopurine pharmacokinetic parameters were different among races, since Latins showed higher plasma concentrations and lower clearance compared to Caucasians. This fact might be due to a different distribution of polymorphisms in genes, other than TPMT, that also influence the pharmacokinetics of mercaptopurine.
How Are Turbulent Sensible Heat Fluxes and Snow Melt Rates Affected by a Changing Snow Cover Fraction?

The complex interaction between the atmospheric boundary layer and the heterogeneous land surface is typically not resolved in numerical models approximating the turbulent heat exchange processes. In this study, we consider the effect of the land surface heterogeneity on the spatial variability of near-surface air temperature fields and on snow melt processes. For this purpose we calculated turbulent sensible heat fluxes and daily snow depth depletion rates with the physics-based surface process model Alpine3D. To account for the effect of a heterogeneous land surface (such as patchy snow covers) on the local energy balance over snow, Alpine3D is driven by two-dimensional atmospheric fields of air temperature and wind velocity, generated with the non-hydrostatic atmospheric model ARPS. The atmospheric model is initialized with a set of snow distributions (snow cover fraction and number of snow patches) and atmospheric conditions (wind velocities) for an idealized flat test site. Numerical results show that the feedback of the heterogeneity of the land surface (snow, no snow) on the near-surface variability of the atmospheric fields result in a significant increase in the mean air temperature ∆TA= 1.8 K (3.7 K, 4.9 K) as the snow cover fraction is decreased from a continuous snow cover to 55 % (25 %, 5 %). Surface turbulent sensible heat fluxes and daily snow depth depletion rates are strongly correlated to mean air temperatures, leading to 22-40 % larger daily snow depth depletion rates for patchy snow covers. Mean air temperatures over snow heavily increase with increasing initial wind velocities and weakly increase with an increasing number of snow patches. Numerical results from the idealized test site are compared with a test site in complex terrain. As slope-induced atmospheric processes (such as the development of katabatic flows) modify turbulent sensible heat fluxes, the variation of the surface energy balance is larger in complex terrain than for an idealized flat test site.
Impact of adherence to cancer-specific prevention recommendations on subsequent risk of cancer in participants in Alberta’s Tomorrow Project

Abstract Objective The World Cancer Research Fund (WCRF) and the American Institute for Cancer Research (AICR) publish recommendations for cancer prevention. The present study aimed to estimate the association between adherence to these cancer-specific prevention recommendations and subsequent development of cancer in a prospective cohort. Design A composite adherence score was constructed based on questionnaire data to reflect overall adherence to WCRF/AICR lifestyle-related recommendations on body fatness, physical activity, diet and alcoholic drinks. Multivariable Cox proportional hazard regression models were used to assess the association (hazard ratio; 95 % CI) between the adherence score and risk of developing cancer. Setting Alberta’s Tomorrow Project, a prospective cohort study. Participants Men and women (n 25 100, mean age at enrolment 50·5 years) recruited between 2001 and 2009 with no previous cancer diagnosis were included in analyses. Results Cancer cases (n 2066) were identified during a mean follow-up of 11·7 years. Participants who were most adherent to the selected WCRF/AICR recommendations (composite score: 4–6) were 13 % (0·87; 0·78, 0·98) less likely to develop cancer compared with those who were least adherent (composite score: 0–2). Each additional recommendation met corresponded to a 5 % (0·95; 0·91, 0·99) reduction in risk of developing cancer. When stratified by sex, the associations remained significant for women, but not for men. Conclusions Adherence to lifestyle-related cancer prevention recommendations was associated with reduced risk of developing cancer over the follow-up term in this Canadian cohort.
Posttraumatic Stress Disorder Symptoms and Problematic Alcohol Use in College Students: The Moderating Role of Alcohol Protective Behavioral Strategies and Gender

Objective: The present study evaluated the moderating role of alcohol protective behavioral strategy subtypes (alcohol PBS; serious harm reduction, manner of drinking, limiting/stopping drinking) and gender on the relationship between posttraumatic stress disorder (PTSD) symptoms and alcohol-related negative consequences. Method: Participants were 2,138 traditional college students (i.e., age between 18 and 25 years old) recruited from 10 universities in the United States who reported drinking in the past month. All participants reported their gender and completed measures of PTSD symptoms, alcohol PBS use, alcohol consumption, and alcohol-related negative consequences through an online survey. Results: Experiencing greater PTSD symptoms was associated with increased alcohol-related negative consequences and all alcohol PBS subtypes were independently associated with fewer alcohol-related negative consequences. Gender had a moderating effect such that the relationship between manner of drinking and alcohol-related negative consequences was weaker among men. Further, we found significant three-way interactions such that the associations between PTSD symptoms and alcohol-related negative consequences were weaker at higher levels of serious harm reduction and limiting/stopping drinking, but only among women. Conclusions: Although alcohol PBS appear beneficial for all college student drinkers, these findings highlight the additional protective value of certain alcohol PBS for college women experiencing PTSD symptoms.
Corticospinal Tract Wiring and Brain Lesion Characteristics in Unilateral Cerebral Palsy: Determinants of Upper Limb Motor and Sensory Function

Brain lesion characteristics (timing, location, and extent) and the type of corticospinal tract (CST) wiring have been proposed as determinants of upper limb (UL) motor function in unilateral cerebral palsy (uCP), yet an investigation of the relative combined impact of these factors on both motor and sensory functions is still lacking. Here, we first investigated whether structural brain lesion characteristics could predict the underlying CST wiring and we explored the role of CST wiring and brain lesion characteristics to predict UL motor and sensory functions in uCP. Fifty-two participants with uCP (mean age (SD): 11 y and 3 m (3 y and 10 m)) underwent a single-pulse Transcranial Magnetic Stimulation session to determine CST wiring between the motor cortex and the more affected hand (n = 17 contralateral, n = 19 ipsilateral, and n = 16 bilateral) and an MRI to determine lesion timing (n = 34 periventricular (PV) lesion, n = 18 corticosubcortical (CSC) lesion), location, and extent. Lesion location and extent were evaluated with a semiquantitative scale. A standardized protocol included UL motor (grip strength, unimanual capacity, and bimanual performance) and sensory measures. A combination of lesion locations (damage to the PLIC and frontal lobe) significantly contributed to differentiate between the CST wiring groups, reclassifying the participants in their original group with 57% of accuracy. Motor and sensory functions were influenced by each of the investigated neurological factors. However, multiple regression analyses showed that motor function was predicted by the CST wiring (more preserved in individuals with contralateral CST (p < 0.01)), lesion extent, and damage to the basal ganglia and thalamus. Sensory function was predicted by the combination of a large and later lesion and an ipsilateral or bilateral CST wiring, which led to increased sensory deficits (p < 0.05). These novel insights contribute to a better understanding of the underlying pathophysiology of UL function and may be useful to delineate individualized treatment strategies.
Reliability and validity of the iSense optical scanner for measuring volume of transtibial residual limb models

Background: Residual limb volume is often measured as part of routine care for people with amputations. These measurements assist in the timing of prosthetic fitting or replacement. In order to make well informed decisions, clinicians need access to measurement tools that are valid and reliable. Objectives: To assess the reliability and criterion validity of the iSense optical scanner in measuring volume of transtibial residual limb models. Study Design: Three assessors performed two measurements each on 13 residual limb models with an iSense optical scanner (3D systems, USA). Intra-rater and inter-rater reliability were calculated using intraclass correlation coefficients. Bland Altman plots were inspected for agreement. Criterion validity was assessed using a steel rod of known dimensions. Ten repeated measurements were performed by one assessor. A t-test was used to determine differences between measured and true rod volume. Results: Intra-rater reliability was excellent (range of intraclass correlation coefficients: 0.991–0.997, all with narrow 95% confidence intervals). While the intraclass correlation coefficients suggest excellent inter-rater reliability between all three assessors (range of intraclass correlation coefficients: 0.952–0.986), the 95% confidence intervals were wide between assessor 3 and the other two assessors. Poor agreement with assessor 3 was also seen in the Bland-Altman plots. Criterion validity was very poor with a significant difference between the mean iSense measurement and the true rod volume (difference: 221.18 mL; p < 0.001). Conclusions: Although intra-rater reliability was excellent for the iSense scanner, we did not find similar results for inter-rater reliability and validity. These results suggest that further testing of the iSense scanner is required prior to use in clinical practice. Clinical relevance The iSense offers a low cost scanning option for residual limb volume measurement. Intra-rater reliability was excellent, but inter-rater reliability and validity were such that clinical adoption is not indicated at present.