Miracle-dz/UniFAR-FTUs huggingface dataset:
Divergent host-plant use promotes reproductive isolation among cynipid gall wasp populations

Ecological speciation occurs when reproductive isolation evolves as a consequence of divergent natural selection among environments. A direct prediction of this process is that ecologically divergent pairs of populations will exhibit greater reproductive isolation than ecologically similar pairs of populations. By comparing allopatric populations of the cynipid gall wasp Belonocnema treatae infesting Quercus virginiana and Quercus geminata, we tested the role that divergent host use plays in generating ecological divergence and sexual isolation. We found differences in body size and gall structure associated with divergent host use, but no difference in neutral genetic divergence between populations on the same or different host plant. We observed significant assortative mating between populations from alternative host plants but not between allopatric populations on the same host plant. Thus, we provide evidence that divergent host use promotes speciation among gall wasp populations.
Statistical Applications in Genetics and Molecular Biology Semi-Parametric Differential Expression Analysis via Partial Mixture Estimation

We develop an approach for microarray differential expression analysis, i.e. identifying genes whose expression levels differ between two or more groups. Current approaches to inference rely either on full parametric assumptions or on permutation-based techniques for sampling under the null distribution. In some situations, however, a full parametric model cannot be justified, or the sample size per group is too small for permutation methods to be valid. We propose a semi-parametric framework based on partial mixture estimation which only requires a parametric assumption for the null (equally expressed) distribution and can handle small sample sizes where permutation methods break down. We develop two novel improvements of Scott's minimum integrated square error criterion for partial mixture estimation [Scott, 2004a,b]. As a side benefit, we obtain interpretable and closed-form estimates for the proportion of EE genes. Pseudo-Bayesian and frequentist procedures for controlling the false discovery rate are given. Results from simulations and real datasets indicate that our approach can provide substantial advantages for small sample sizes over the SAM method of Tusher et al. [2001], the empirical Bayes procedure of Efron and Tibshirani [2002], the mixture of normals of Pan et al. [2003] and a t-test with p-value adjustment [Dudoit et al., 2003] to control the FDR [Benjamini and Hochberg, 1995].
TEACHING FOR TRANSFER: INSIGHTS FROM THEORY AND PRACTICES IN PRIMARY-LEVEL FRENCH-SECOND-LANGUAGE CLASSROOMS

This paper illustrates teaching for transfer across languages by synthesizing key insights from theory and previously published research alongside our case study data from primary-level teachers in core French-second-language (CF) classrooms in Ontario, Canada. Drawing on research that redefines language transfer as a resource, this study drew on several influential theoretical notions and data collected through interviews and classroom observations. All of these sources point to a multi-leveled approach to teaching for transfer that includes considerations of learning, teaching and contextual features. Study data suggest that CF teachers plan for transfer and use a range of strategies likely to promote its use with students. This paper connects theory, research and practice with the aim of strengthening dialogue among researchers and educators.
Promoting linguistic complexity, greater message length and ease of engagement in email writing in people with aphasia: initial evidence from a study utilizing assistive writing software.

BACKGROUND Improving email writing in people with aphasia could enhance their ability to communicate, promote interaction and reduce isolation. Spelling therapies have been effective in improving single-word writing. However, there has been limited evidence on how to achieve changes to everyday writing tasks such as email writing in people with aphasia. One potential area that has been largely unexplored in the literature is the potential use of assistive writing technologies, despite some initial evidence that assistive writing software use can lead to qualitative and quantitative improvements to spontaneous writing. AIMS This within-participants case series design study aimed to investigate the effects of using assistive writing software to improve email writing in participants with dysgraphia related to aphasia. METHODS & PROCEDURES Eight participants worked through a hierarchy of writing tasks of increasing complexity within broad topic areas that incorporate the spheres of writing need of the participants: writing for domestic needs, writing for social needs and writing for business/administrative needs. Through completing these tasks, participants had the opportunity to use the various functions of the software, such as predictive writing, word banks and text to speech. Therapy also included training and practice in basic computer and email skills to encourage increased independence. Outcome measures included email skills, keyboard skills, email writing and written picture description tasks, and a perception of disability assessment. OUTCOMES & RESULTS Four of the eight participants showed statistically significant improvements to spelling accuracy within emails when using the software. At a group level there was a significant increase in word length with the software; while four participants showed noteworthy changes to the range of word classes used. Enhanced independence in email use and improvements in participants' perceptions of their writing skills were also noted. CONCLUSIONS & IMPLICATIONS This study provided some initial evidence that assistive writing technologies can support people with aphasia in email writing across a range of important performance parameters. However, more research is needed to measure the effects of these technologies on the writing of people with aphasia, and to determine the optimal compensatory mechanisms for specific people given the linguistic-strategic resources they bring to the task of email writing.
The Hidden Snake in the Grass: Superior Detection of Snakes in Challenging Attentional Conditions

Snakes have provided a serious threat to primates throughout evolution. Furthermore, bites by venomous snakes still cause significant morbidity and mortality in tropical regions of the world. According to the Snake Detection Theory (SDT Isbell, 2006; 2009), the vital need to detect camouflaged snakes provided strong evolutionary pressure to develop astute perceptual capacity in animals that were potential targets for snake attacks. We performed a series of behavioral tests that assessed snake detection under conditions that may have been critical for survival. We used spiders as the control stimulus because they are also a common object of phobias and rated negatively by the general population, thus commonly lumped together with snakes as “evolutionary fear-relevant”. Across four experiments (N = 205) we demonstrate an advantage in snake detection, which was particularly obvious under visual conditions known to impede detection of a wide array of common stimuli, for example brief stimulus exposures, stimuli presentation in the visual periphery, and stimuli camouflaged in a cluttered environment. Our results demonstrate a striking independence of snake detection from ecological factors that impede the detection of other stimuli, which suggests that, consistent with the SDT, they reflect a specific biological adaptation. Nonetheless, the empirical tests we report are limited to only one aspect of this rich theory, which integrates findings across a wide array of scientific disciplines.
ASYMMETRIC LEAVES2-LIKE19/LATERAL ORGAN BOUNDARIES DOMAIN30 and ASL20/LBD18 Regulate Tracheary Element Differentiation in Arabidopsis[W]

ASYMMETRIC LEAVES2 (AS2)/LATERAL ORGAN BOUNDARIES DOMAIN (LBD) family proteins are plant-specific nuclear proteins, and genes encoding several family members have been implicated in plant development. We investigated the function of two members of the Arabidopsis thaliana AS2/LBD family, AS2-LIKE19 (ASL19)/LBD30 and ASL20/LBD18, which encode homologous proteins. Both ASL19 and ASL20 were expressed in immature tracheary elements (TEs), and the expression was dependent on VASCULAR-RELATED NAC-DOMAIN PROTEIN6 (VND6) and VND7, which are transcription factors required for TE differentiation. Overexpression of ASL19 and ASL20 induced transdifferentiation of cells from nonvascular tissues into TE-like cells, similar to those induced upon VND6/7 overexpression. By contrast, aberrant TEs were formed when a cDNA encoding a fusion protein of ASL20 with an artificial repressor domain (ASL20-SRDX) was expressed from its native promoter. These results provide evidence that ASL proteins positively regulate TE differentiation. In transgenic plants overexpressing both ASL19 and ASL20, the xylem-deficient phenotype caused by the expression of dominant-negative versions of VND6/7 proteins was not rescued. However, ectopic expression of VND7 was detected in plants overexpressing ASL20. Moreover, VND genes and their downstream targets were downregulated in ASL20-SRDX plants. Therefore, ASL20 appears to be involved in a positive feedback loop for VND7 expression that regulates TE differentiation-related genes.
Influences of the Atlantic Warm Pool on Western Hemisphere Summer Rainfall and Atlantic Hurricanes

The Atlantic warm pool (AWP) of water warmer than 28.5°C comprises the Gulf of Mexico, the Caribbean Sea, and the western tropical North Atlantic (TNA). The AWP reaches its maximum size around September, with large AWPs being almost 3 times larger than small ones. Although ENSO teleconnections are influential on the AWP, about two-thirds of the large and small AWP variability appears unrelated to ENSO. The AWP is usually geographically different from the TNA; however, the AWP size is correlated with the TNA SST anomalies. During August to October, large AWPs and warm TNA are associated with increased rainfall over the Caribbean, Mexico, the eastern subtropical Atlantic, and the southeast Pacific, and decreased rainfall in the northwest United States, Great Plains, and eastern South America. In particular, rainfall in the Caribbean, Central America, and eastern South America from August to October is mainly related to the size of the AWP. Large (small) AWPs and warm (cold) TNA correspond to a weakening (strengthening) of the northward surface winds from the AWP to the Great Plains that disfavors (favors) moisture transport for rainfall over the Great Plains. On the other hand, large (small) AWPs and warm (cold) TNA strengthen (weaken) the summer regional Atlantic Hadley circulation that emanates from the warm pool region into the southeast Pacific, changing the subsidence over the southeast Pacific and thus the stratus cloud and drizzle there. The large AWP, associated with a decrease in sea level pressure and an increase in atmospheric convection and cloudiness, corresponds to a weak tropospheric vertical wind shear and a deep warm upper ocean, and thus increases Atlantic hurricane activity.
Reduced-Complexity Coherent Versus Non-Coherent QAM-Aided Space-Time Shift Keying

A novel reduced-complexity near-optimal detection algorithm is proposed for enhancing the recent Coherently-detected Space-Time Shift Keying (CSTSK) scheme employing arbitrary constellations, such as {\cal L}-point Phase-Shift Keying (PSK) and Quadrature Amplitude Modulation (QAM). The proposed detector relies on a modified Matched Filter (MF) concept. More specifically, we exploit both the constellation diagram of the modulation scheme employed as well as the Inter-Element-Interference (IEI)-free STSK architecture. Furthermore, we generalize the Pulse Amplitude Modulation (PAM)- or PSK-aided Differentially-encoded STSK (DSTSK) concept and conceive its more bandwidth-efficient QAM-aided counterpart. Then, the proposed reduced-complexity CSTSK detector is applied to the QAM-aided DSTSK scheme, which enables us to carry out low-complexity non-coherent detection, while dispensing with channel estimation. It is revealed that the proposed detector is capable of approaching the optimal Maximum Likelihood (ML) detector's performance, while avoiding the exhaustive ML search. Interestingly, our simulation results also demonstrate that the reduced-complexity detector advocated may achieve the same performance as that of the optimal ML detector for the specific STSK scheme's parameters. Another novelty of this paper is that the star-QAM STSK scheme tends to outperform its square-QAM counterpart, especially for high number of dispersion matrices. Furthermore, we provided both the theoretical analysis and the simulations, in order to support this unexpected fact.
On affine rigidity

We study the properties of affine rigidity of a hypergraph and prove a variety of fundamental results. First, we show that affine rigidity is a generic property (i.e., depends only on the hypergraph, not the particular embedding). Then we prove that a graph is generically neighborhood affinely rigid in d -dimensional space if it is ( d +1)-vertex-connected. We also show neighborhood affine rigidity of a graph implies universal rigidity of its squared graph. Our results, and affine rigidity more generally, have natural applications in point registration and localization, as well as connections to manifold learning.
A Review of Innovations in Rhegmatogenous Retinal Detachment Surgical Techniques

Rhegmatogenous retinal detachment (RRD) requires surgical intervention for its repair. There are variable techniques used for this purpose, and they are all being continuously refined. In this review, we detail the recent innovations in surgical management of RRD and proliferative vitreoretinopathy (PVR).
Quantitative immunoelectrophoretic analysis of human antibodies against herpes simplex virus antigens

By use of crossed immunoelectrophoresis with intermediate gel, antidbody titers against six individual herpes simplex virus (HSV) glycoproteins and two nonglycosylated proteins were determined in 100 human sera. High antibody titers were found against two different HSV type-common glycoproteins designated Ag8 and Ag11 (containing glycosylated polypeptides D and B, respectively). The anti-Ag8 and -Ag11 titers correlated with HSV neutralizing antibody titers. Most of the serological cross-reactivity between HSV type 1 and type 2 was probably caused by antibodies to Ag8 and Ag11. Human antibodies against one HSV type 1-specific glycoprotein (Ag6, containing glycosylated polypeptide C) and two HSV type 2 glycoproteins (Ag4 and Ag9) were also demonstrated, and the titers correlated better with neutralizing antibody titers of the homologous than of the heterologous virus type. The data presented can be directly applied to the further development of diagnostic reagents.
The Global Historical Climatology Network Monthly Temperature Dataset, Version 4

We describe a fourth version of the Global Historical Climatology Network (GHCN)-monthly (GHCNm) temperature dataset. Version 4 (v4) fulfills the goal of aligning GHCNm temperature values with the GHCN-daily dataset and makes use of data from previous versions of GHCNm as well as data collated under the auspices of the International Surface Temperature Initiative. GHCNm v4 has many thousands of additional stations compared to version 3 (v3) both historically and with short time-delay updates. The greater number of stations as well as the use of records with incomplete data during the base period provides for greater global coverage throughout the record compared to earlier versions. Like v3, the monthly averages are screened for random errors and homogenized to address systematic errors. New to v4, uncertainties are calculated for each station series, and regional uncertainties scale directly from the station uncertainties. Correlated errors in the station series are quantified by running the homogenization algorithm as an ensemble. Additional uncertainties associated with incomplete homogenization and use of anomalies are then incorporated into the station ensemble. Further uncertainties are quantified at the regional level, the most important of which is for incomplete spatial coverage. Overall, homogenization has a smaller impact on the v4 global trend compared to v3, though adjustments lead to much greater consistency than between the unadjusted versions. The adjusted v3 global mean therefore falls within the range of uncertainty for v4 adjusted data. Likewise, annual anomaly uncertainties for the other major independent land surface air temperature datasets overlap with GHCNm v4 uncertainties.
Revisiting Bayesian blind deconvolution

Blind deconvolution involves the estimation of a sharp signal or image given only a blurry observation. Because this problem is fundamentally ill-posed, strong priors on both the sharp image and blur kernel are required to regularize the solution space. While this naturally leads to a standard MAP estimation framework, performance is compromised by unknown trade-off parameter settings, optimization heuristics, and convergence issues stemming from non-convexity and/or poor prior selections. To mitigate some of these problems, a number of authors have recently proposed substituting a variational Bayesian (VB) strategy that marginalizes over the high-dimensional image space leading to better estimates of the blur kernel. However, the underlying cost function now involves both integrals with no closed-form solution and complex, function-valued arguments, thus losing the transparency of MAP. Beyond standard Bayesian-inspired intuitions, it thus remains unclear by exactly what mechanism these methods are able to operate, rendering understanding, improvements and extensions more difficult. To elucidate these issues, we demonstrate that the VB methodology can be recast as an unconventional MAP problem with a very particular penalty/prior that conjoins the image, blur kernel, and noise level in a principled way. This unique penalty has a number of useful characteristics pertaining to relative concavity, local minima avoidance, normalization, and scale-invariance that allow us to rigorously explain the success of VB including its existing implementational heuristics and approximations. It also provides strict criteria for learning the noise level and choosing the optimal image prior that, perhaps counter-intuitively, need not reflect the statistics of natural scenes. In so doing we challenge the prevailing notion of why VB is successful for blind deconvolution while providing a transparent platform for introducing enhancements and extensions. Moreover, the underlying insights carry over to a wide variety of other bilinear models common in the machine learning literature such as independent component analysis, dictionary learning/sparse coding, and non-negative matrix factorization.
Metabolic syndrome in Finnish women 7 years after a gestational diabetes prevention trial

Background Risk for developing metabolic syndrome (MeS) after delivery is high among women with gestational diabetes mellitus (GDM), but little is known about development of MeS among women with risk factors for GDM during pregnancy. In the present study, we studied the prevalence of MeS 7 years postpartum among women with GDM risk factors during pregnancy, women with early GDM diagnosis and women without GDM risk factors. We also analysed the early pregnancy risk factors associated with MeS. Methods A Finnish cluster randomised controlled GDM prevention trial was conducted in 2007–2009. The prevalence of MeS according to International Diabetes Federation criteria was determined in the follow-up study 7 years after original trial. Eligible participants (n=289) in 4 study groups (intervention (n=83) and usual care (n=87) with GDM risk factors; early GDM (n=51), and healthy control without GDM risk factors (n=68)) were evaluated for MeS. Binary logistic regression models were used to analyse risk factors associated with MeS. Results 7 years postpartum, the MeS prevalence was 14% (95% CI 8% to 25%) in the intervention group; 15% (CI 8% to 25%) in the usual care group; 50% (CI 35% to 65%) in the early GDM group and 7% (CI 2% to 18%) in the healthy control group. OR for MeS in women with GDM risk factors did not differ from the healthy control group. Body mass index (BMI)-adjusted OR for MeS was 9.18 (CI 1.82 to 46.20) in the early GDM group compared with the healthy control group. Increased prepregnancy BMI was associated with MeS (OR, 1.17, CI 1.08 to 1.28, adjusted for group). Conclusions Increased prepregnancy BMI and early GDM diagnosis were the strongest risk factors for developing MeS 7 years postpartum. Overweight and obese women and especially those with early GDM should be monitored and counselled for cardiometabolic risk factors after delivery.
Benefits of a Contextual Approach to Understanding and Treating Complex Trauma

ABSTRACT The conceptual framework and treatment rationale of contextual therapy are described. Contextual therapy was specifically fashioned for survivors of prolonged child abuse (PCA). It is grounded in the observation that contexts beyond abuse trauma, especially restrictions in psychological development stemming from growing up in an ineffective family environment, appreciably impact the adjustment of many PCA survivors. Contextual therapy proposes that remediation of developmental gaps commonly manifested by PCA survivors is essential to equip them to (a) benefit from rather than be debilitated by trauma processing and (b) move beyond symptom reduction to the attainment of adequate social and occupational functioning.
Production and Actions of Hydrogen Sulfide, a Novel Gaseous Bioactive Substance, in the Kidneys

Hydrogen sulfide (H2S), a novel endogenous gaseous bioactive substance, has recently been implicated in the regulation of cardiovascular and neuronal functions. However, its role in the control of renal function is unknown. In the present study, incubation of renal tissue homogenates with l-cysteine (l-Cys) (as a substrate) produced H2S in a concentration-dependent manner. This H2S production was completely abolished by inhibition of both cystathionine β-synthetase (CBS) and cystathionine γ-lyase (CGL), two major enzymes for the production of H2S, using amino-oxyacetic acid (AOAA), an inhibitor of CBS, and propargylglycine (PPG), an inhibitor of CGL. However, inhibition of CBS or CGL alone induced a small decrease in H2S production. In anesthetized Sprague-Dawley rats, intrarenal arterial infusion of an H2S donor (NaHS) increased renal blood flow, glomerular filtration rate (GFR), urinary sodium (UNa·V), and potassium (UK·V) excretion. Consistently, infusion of both AOAA and PPG to inhibit the endogenous H2S production decreased GFR, UNa·V, and UK·V, and either one of these inhibitors alone had no significant effect on renal functions. Infusion of l-Cys into renal artery to increase the endogenous H2S production also increased GFR, UNa·V, and UK·V, which was blocked by AOAA plus PPG. It was shown that H2S had both vascular and tubular effects and that the tubular effect of H2S might be through inhibition of Na+/K+/2Cl- cotransporter and Na+/K+/ATPase activity. These results suggest that H2S participates in the control of renal function and increases urinary sodium excretion via both vascular and tubular actions in the kidney.