Miracle-dz/UniFAR-FTUs huggingface dataset:
PIK3CA mutations, PTEN, and pHER2 expression and impact on outcome in HER2-positive early-stage breast cancer patients treated with adjuvant chemotherapy and trastuzumab.

BACKGROUND This study was conducted to determine the frequency of PIK3CA mutations and human epidermal growth factor receptor-2 (HER2) phosphorylation status (pHER2-Tyr1221/1222) and if PIK3CA, phosphatase and tensin homolog (PTEN), or pHER2 has an impact on outcome in HER2-positive early-stage breast cancer patients treated with adjuvant chemotherapy and trastuzumab. PATIENTS AND METHODS Two hundred and forty HER2-positive early-stage breast cancer patients receiving adjuvant treatment (cyclophosphamide 600 mg/m2, epirubicin 60 mg/m2, and fluorouracil 600 mg/m2) before administration of 1 year trastuzumab were assessable. PTEN and pHER2 expression were assessed by immunohistochemistry. PIK3CA mutations (exons 9 and 20) were determined by pyrosequencing. RESULTS Five-year overall survival (OS) and invasive disease-free survival were 87.8% and 81.0%, respectively. Twenty-six percent of patients had a PIK3CA mutation, 24% were PTEN low, 45% pHER2 high, and 47% patients had increased PI3K pathway activation (PTEN low and/or PIK3CA mutation). No significant correlations were observed between the clinicopathological variables and PIK3CA, PTEN, and pHER2 status. In both univariate and multivariate analyses, patients with PIK3CA mutations or high PI3K pathway activity had a significant worse OS [multivariate: hazard ratio (HR) 2.14, 95% confidence interval (CI) 1.01-4.51, P=0.046; and HR 2.35, 95% CI 1.10-5.04, P=0.03]. CONCLUSION Patients with PIK3CA mutations or increased PI3K pathway activity had a significantly poorer survival despite adequate treatment with adjuvant chemotherapy and trastuzumab.
A Primate APOL1 Variant That Kills Trypanosoma brucei gambiense

Humans are protected against infection from most African trypanosomes by lipoprotein complexes present in serum that contain the trypanolytic pore-forming protein, Apolipoprotein L1 (APOL1). The human-infective trypanosomes, Trypanosoma brucei rhodesiense in East Africa and T. b. gambiense in West Africa have separately evolved mechanisms that allow them to resist APOL1-mediated lysis and cause human African trypanosomiasis, or sleeping sickness, in man. Recently, APOL1 variants were identified from a subset of Old World monkeys, that are able to lyse East African T. b. rhodesiense, by virtue of C-terminal polymorphisms in the APOL1 protein that hinder that parasite’s resistance mechanism. Such variants have been proposed as candidates for developing therapeutic alternatives to the unsatisfactory anti-trypanosomal drugs currently in use. Here we demonstrate the in vitro lytic ability of serum and purified recombinant protein of an APOL1 ortholog from the West African Guinea baboon (Papio papio), which is able to lyse examples of all sub-species of T. brucei including T. b. gambiense group 1 parasites, the most common agent of human African trypanosomiasis. The identification of a variant of APOL1 with trypanolytic ability for both human-infective T. brucei sub-species could be a candidate for universal APOL1-based therapeutic strategies, targeted against all pathogenic African trypanosomes.
Variability among species of stomatal control under fluctuating soil water status and evaporative demand: modelling isohydric and anisohydric behaviours

Stomatal control of species with contrasting stomatal behaviours have been investigated under natural fluctuations of evaporative demand and soil water status. Sunflower and barley (anisohydric behaviour) have a daytime leaf water potential (ψ l ) which markedly decreases with evaporative demand during the day and is lower in droughted than in watered plants. In contrast, maize and poplar (isohydric behaviour) maintain a nearly constant ψ l during the day at a value which does not depend on soil water status until plants are close to death. Plants were also subjected to a range of soil water potentials under contrasting air vapour pressure deficits (VPD, from 0.5 to 3 kPa) in the field, in the greenhouse or in a growth chamber. Finally, plants or detached leaves were fed with varying concentrations of artificial ABA. Stomatal conductance of well-watered plants had no response to VPD when plants were grown in natural soils, suggesting that the opposite result observed in many laboratory experiments might be linked to the low unsaturated hydraulic conductivity of usual potting substrates. The response of stomatal conductance of all studied species to the concentration of ABA in pressurized xylem sap ([ABA] xyl ) was the same whether ABA had an endogenous origin (droughted plants) or was artificially fed. However stomatal response of maize and poplar to [ABA] xyl markedly changed with varying evaporative demand or ψ l , whereas this was not the case in sunflower or barley. This suggests that isohydric behaviour is linked to an interaction between hydraulic and chemical information, while anisohydric behaviour is linked to an absence of interaction. In all cases, [ABA] xyl was related to soil water status with common relationships for different experimental conditions, but with markedly different responses among species. Diurnal variations of [ABA] xyl with evaporative demand were small in all studied species. Results are synthesized in a model which accounts for observed behaviours of g s , ψ l and [ABA] xyl in fluctuating conditions and for several species. The validity of this model, in particular the physiological meaning of [ABA] xyl , is discussed.
Dynamic control set-model predictive control for field-oriented control of VSI-PMSM

In this digest, a novel Model Predictive Control scheme is proposed for 2L-VSI PMSM drive system. Even though standard FCS-MPC can lead to low switching frequency, but it degrades the steady state performance, while MPC with duty cycle reduces the current and torque ripples at expense of high switching frequency. To mollify the contradiction between the steady-state performance and the switching frequency, the proposed approach can move the switching instant from sampling instant to any instant within a sampling interval. But variable switching instant also introduces infinite candidate control actions, which can compose a dynamic control set. To capture the optimal control action, variable switching instant is transformed as vectoral form, and the convey quadratic relationship between objective function and variable switching instant is derived. Based on it, an online optimization procedure is established. Finally, the test results show that the proposed approach can reach a balance between steady-state performance and switching frequency.
Impact of Ground Plane Doping and Bottom-Gate Biasing on Electrical Properties in In0.53Ga0.47As-OI MOSFETs and Donor Wafer Reusability Toward Monolithic 3-D Integration With In0.53Ga0.47As Channel

In this paper, we fabricated In<sub>0.53</sub>Ga<sub>0.47</sub>As-on insulator (OI) MOSFETs on Si substrates with different doping types to mimic ground plane doping using direct wafer bonding and epitaxial lift-off (ELO) techniques. We investigated the impact of doping types on the ground plane and the backgate biasing, which are important and preferable components in monolithic 3-D (M3D) integration, on the electrical properties of MOSFETs, such as the threshold voltage (<inline-formula> <tex-math notation="LaTeX">${V} _{T}$ </tex-math></inline-formula>) and the effective mobility (<inline-formula> <tex-math notation="LaTeX">$\mu _{\textsf {eff}}$ </tex-math></inline-formula>). It was found that <inline-formula> <tex-math notation="LaTeX">${V} _{T}$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$\mu _{\textsf {eff}}$ </tex-math></inline-formula> were significantly modulated by the backsubstrate doping and the backbiasing. These observations were explained by the change of carrier distributions, which were confirmed by technology computer-aided design simulation. Furthermore, we investigated the reusability of InP donor substrates for sequential epitaxial growth after ELO process toward a cost-effective M3D integration with the In<sub>0.53</sub>Ga<sub>0.47</sub>As channel.
Shared control of human and robot by approximate dynamic programming

In this paper, a framework of human-robot shared control is developed based on finding the solution to an optimization problem. Human dynamics are taken into account in the analysis of the coupled human-robot system, and objectives of both human and robot are considered. Approximate dynamic programming is employed to solve the optimization problem in the presence of unknown human and robot dynamics. The validity of the proposed method is verified through simulation studies.
Relationship between bilirubin concentration, coronary endothelial function, and inflammatory stress in overweight patients.

AIM Bilirubin has antioxidant properties and may protect against atherosclerosis and coronary heart disease (CHD). Further, in patients with metabolic syndrome, hyperbilirubinemia is associated with attenuation of insulin resistance. The aim of the present study was to determine the relationship between serum bilirubin concentration and coronary endothelial function in overweight patients. METHODS The study population consisted of 107 patients without CHD who underwent coronary flow studies. Vascular reactivity was examined by intra-coronary administration of papaverine and nitroglycerin. Coronary endothelial function was evaluated by assessing the change in coronary artery diameter to papaverine [percent change in flow-mediated dilatation (%FMD)] and nitroglycerin (%NTG). Serum total bilirubin, high-sensitivity C-reactive protein (hs-CRP), high density lipoprotein-cholesterol (HDL-C), fasting plasma glucose and immunoreactive insulin levels were also measured, and the homeostasis model assessment insulin resistance (HOMA-IR) index was calculated. Patients were divided into two groups according to body mass index (BMI): an overweight group (BMI ≥ 25; n = 36) and a normal weight group (BMI < 25; n = 71). RESULTS In the overweight group, univariate analysis revealed that log-transformed total bilirubin was positively correlated with %FMD and HDL-C (r = 0.38, p< 0.05; r = 0.30, p < 0.05, respectively) and was inversely correlated with log-transformed hs-CRP and HOMA-IR (r = -0.45, p < 0.01; r = -0.45, p< 0.05, respectively). Multivariate analysis revealed that log-transformed hs-CRP was the only independent predictor of log-transformed total bilirubin (p< 0.05). CONCLUSIONS These results suggest that a high bilirubin level was associated with favorable coronary endothelial function in overweight patients. Further, the anti-inflammatory effects of bilirubin may mediate this effect.
Lifestyle changes and the risk of developing endometrial and ovarian cancers: opportunities for prevention and management

Modifiable lifestyle factors, such as obesity, lack of physical activity, and smoking, contribute greatly to cancer and chronic disease morbidity and mortality worldwide. This review appraises recent evidence on modifiable lifestyle factors in the prevention of endometrial cancer (EC) and ovarian cancer (OC) as well as new evidence for lifestyle management of EC and OC survivors. For EC, obesity continues to be the strongest risk factor, while new evidence suggests that physical activity, oral contraceptive pills, and bariatric surgery may be protective against EC. Other medications, such as metformin and nonsteroidal anti-inflammatory drugs, may be protective, and interventional research is ongoing. For OC, we find increasing evidence to support the hypothesis that obesity and hormone replacement therapy increase the risk of developing OC. Oral contraceptive pills are protective against OC but are underutilized. Dietary factors such as the Mediterranean diet and alcohol consumption do not seem to affect the risk of either OC or EC. For EC and OC survivors, physical activity and weight loss are associated with improved quality of life. Small interventional trials show promise in increasing physical activity and weight maintenance for EC and OC survivors, although the impact on long-term health, including cancer recurrence and overall mortality, is unknown. Women’s health providers should integrate counseling about these modifiable lifestyle factors into both the discussion of prevention for all women and the management of survivors of gynecologic cancers.
Posture Affects How Robots and Infants Map Words to Objects

For infants, the first problem in learning a word is to map the word to its referent; a second problem is to remember that mapping when the word and/or referent are again encountered. Recent infant studies suggest that spatial location plays a key role in how infants solve both problems. Here we provide a new theoretical model and new empirical evidence on how the body – and its momentary posture – may be central to these processes. The present study uses a name-object mapping task in which names are either encountered in the absence of their target (experiments 1–3, 6 & 7), or when their target is present but in a location previously associated with a foil (experiments 4, 5, 8 & 9). A humanoid robot model (experiments 1–5) is used to instantiate and test the hypothesis that body-centric spatial location, and thus the bodies’ momentary posture, is used to centrally bind the multimodal features of heard names and visual objects. The robot model is shown to replicate existing infant data and then to generate novel predictions, which are tested in new infant studies (experiments 6–9). Despite spatial location being task-irrelevant in this second set of experiments, infants use body-centric spatial contingency over temporal contingency to map the name to object. Both infants and the robot remember the name-object mapping even in new spatial locations. However, the robot model shows how this memory can emerge –not from separating bodily information from the word-object mapping as proposed in previous models of the role of space in word-object mapping – but through the body’s momentary disposition in space.
Practical, Real-Time, and Robust Watermarking on the Spatial Domain for High-Definition Video Contents

Commercial markets employ digital right management (DRM) systems to protect valuable high-definition (HD) quality videos. DRM system uses watermarking to provide copyright protection and ownership authentication of multimedia contents. We propose a real-time video watermarking scheme for HD video in the uncompressed domain. Especially, our approach is in aspect of practical perspectives to satisfy perceptual quality, real-time processing, and robustness requirements. We simplify and optimize human visual system mask for real-time performance and also apply dithering technique for invisibility. Extensive experiments are performed to prove that the proposed scheme satisfies the invisibility, real-time processing, and robustness requirements against video processing attacks. We concentrate upon video processing attacks that commonly occur in HD quality videos to display on portable devices. These attacks include not only scaling and low bit-rate encoding, but also malicious attacks such as format conversion and frame rate change.
Does Breastfeeding Help to Reduce the Risk of Childhood Overweight and Obesity? A Propensity Score Analysis of Data from the KiGGS Study

Background Current studies suggest that the beneficial effect of breastfeeding on overweight and obesity may have been largely overestimated. We examined the relationship between >4 months of full breastfeeding and overweight/obesity in children living in Germany. Methods We analyzed retrospectively collected data on breastfeeding from children aged 3–17 years who participated in the German Health Interview and Examination Survey for Children and Adolescents (KiGGS baseline study) between 2003 and 2006 (n = 13163). To minimize confounding, we applied propensity score matching and multivariate logistic regression analyses to estimate the effect of breastfeeding on childhood overweight and obesity. Results Adjusted analyses of the matched dataset (n = 8034) indicated that children who were breastfed for <4 months had a significant reduction in the odds of overweight (OR 0.81 [95% CI 0.71–0.92]) and obesity (OR 0.75 [95% CI 0.61–0.92]) compared to children who were not breastfed or who were breastfed for a shorter duration. Further analyses stratified by age group showed that the association was strongest in children aged 7–10 years (OR 0.67 [95% CI 0.53–0.84] for overweight and OR 0.56 [95% CI 0.39–0.81] for obesity), while no significant effect could be seen in other age groups. Discussion Our findings support the hypothesis that breastfeeding does have a beneficial effect on childhood overweight and obesity, although the effect seems to be strongest in children of primary school age.
Temporal Lobe Cortical Thickness Correlations Differentiate the Migraine Brain from the Healthy Brain

Background Interregional cortical thickness correlations reflect underlying brain structural connectivity and functional connectivity. A few prior studies have shown that migraine is associated with atypical cortical brain structure and atypical functional connectivity amongst cortical regions that participate in sensory processing. However, the specific brain regions that most accurately differentiate the migraine brain from the healthy brain have yet to be determined. The aim of this study was to identify the brain regions that comprised interregional cortical thickness correlations that most differed between migraineurs and healthy controls. Methods This was a cross-sectional brain magnetic resonance imaging (MRI) investigation of 64 adults with migraine and 39 healthy control subjects recruited from tertiary-care medical centers and their surrounding communities. All subjects underwent structural brain MRI imaging on a 3T scanner. Cortical thickness was determined for 70 brain regions that cover the cerebral cortex and cortical thickness correlations amongst these regions were calculated. Cortical thickness correlations that best differentiated groups of six migraineurs from controls and vice versa were identified. Results A model containing 15 interregional cortical thickness correlations differentiated groups of migraineurs from healthy controls with high accuracy. The right temporal pole was involved in 13 of the 15 interregional correlations while the right middle temporal cortex was involved in the other two. Conclusions A model consisting of 15 interregional cortical thickness correlations accurately differentiates the brains of small groups of migraineurs from those of healthy controls. Correlations with the right temporal pole were highly represented in this classifier, suggesting that this region plays an important role in migraine pathophysiology.
The effect of tree nut, peanut, and soy nut consumption on blood pressure: a systematic review and meta-analysis of randomized controlled clinical trials.

BACKGROUND Although several studies have assessed the effects of nut consumption (tree nuts, peanuts, and soy nuts) on blood pressure (BP), the results are conflicting. OBJECTIVE The aim was to conduct a systematic review and meta-analysis of published randomized controlled trials (RCTs) to estimate the effect of nut consumption on BP. DESIGN The databases MEDLINE, SCOPUS, ISI Web of Science, and Google Scholar were searched for RCTs carried out between 1958 and October 2013 that reported the effect of consuming single or mixed nuts (including walnuts, almonds, pistachios, cashews, hazelnuts, macadamia nuts, pecans, peanuts, and soy nuts) on systolic BP (SBP) or diastolic BP (DBP) as primary or secondary outcomes in adult populations aged ≥18 y. Relevant articles were identified by screening the abstracts and titles and the full text. Studies that evaluated the effects for <2 wk or in which the control group ingested different healthy oils were excluded. Mean ± SD changes in SBP and DBP in each treatment group were recorded for meta-analysis. RESULTS Twenty-one RCTs met the inclusion criteria. Our findings suggest that nut consumption leads to a significant reduction in SBP in participants without type 2 diabetes [mean difference (MD): -1.29; 95% CI: -2.35, -0.22; P = 0.02] but not in the total population. Subgroup analyses of different nut types suggest that pistachios, but not other nuts, significantly reduce SBP (MD: -1.82; 95% CI: -2.97, -0.67; P = 0.002). Our study suggests that pistachios (MD: -0.80; 95% CI: -1.43, -0.17; P = 0.01) and mixed nuts (MD: -1.19; 95% CI: -2.35, -0.03; P = 0.04) have a significant reducing effect on DBP. We found no significant changes in DBP after the consumption of other nuts. CONCLUSIONS Total nut consumption lowered SBP in participants without type 2 diabetes. Pistachios seemed to have the strongest effect on reducing SBP and DBP. Mixed nuts also reduced DBP.
Correction of estimates of retention in care among a cohort of HIV-positive patients in Uganda in the period before starting ART: a sampling-based approach

Objective The aim of this study was to use a sampling-based approach to obtain estimates of retention in HIV care before initiation of antiretroviral treatment (ART), corrected for outcomes in patients who were lost according to clinic registers. Design Retrospective cohort study of HIV-positive individuals not yet eligible for ART (CD4 >500). Setting Three urban and three rural HIV care clinics in Uganda; information was extracted from the clinic registers for all patients who had registered for pre-ART care between January and August 2015. Participants A random sample of patients who were lost according to the clinic registers (>3 months late to scheduled visit) was traced to ascertain their outcomes. Outcome measures The proportion of patients lost from care was estimated using a competing risks approach, first based on the information in the clinic records alone and then using inverse probability weights to incorporate the results from tracing. Cox regression was used to determine factors associated with loss from care. Results Of 1153 patients registered for pre-ART care (68% women, median age 29 years, median CD4 count 645 cells/µL), 307 (27%) were lost according to clinic records. Among these, 195 (63%) were selected for tracing; outcomes were ascertained in 118 (61%). Seven patients (6%) had died, 40 (34%) were in care elsewhere and 71 (60%) were out of care. Loss from care at 9 months was 30.2% (95% CI 27.3% to 33.5%). After incorporating outcomes from tracing, loss from care decreased to 18.5% (95% CI 13.8% to 23.6%). Conclusion Estimates of loss from HIV care may be too high if based on routine clinic data alone. A sampling-based approach is a feasible way of obtaining more accurate estimates of retention, accounting for transfers to other clinics.
Evidence from molecular dynamics simulations of conformational preorganization in the ribonuclease H active site

Ribonuclease H1 (RNase H) enzymes are well-conserved endonucleases that are present in all domains of life and are particularly important in the life cycle of retroviruses as domains within reverse transcriptase. Despite extensive study, especially of the E. coli homolog, the interaction of the highly negatively charged active site with catalytically required magnesium ions remains poorly understood. In this work, we describe molecular dynamics simulations of the E. coli homolog in complex with magnesium ions, as well as simulations of other homologs in their apo states. Collectively, these results suggest that the active site is highly rigid in the apo state of all homologs studied and is conformationally preorganized to favor the binding of a magnesium ion. Notably, representatives of bacterial, eukaryotic, and retroviral RNases H all exhibit similar active-site rigidity, suggesting that this dynamic feature is only subtly modulated by amino acid sequence and is primarily imposed by the distinctive RNase H protein fold.