Miracle-dz/UniFAR-FTUs huggingface dataset:
The human RAP1 and GFAPɛ proteins increase γ-secretase activity in a yeast model system

Abstract Alzheimer's disease (AD) is an age-related disorder that results in progressive cognitive impairment and memory loss. Deposition of amyloid β (Aβ) peptides in senile plaques is a hallmark of AD. γ-secretase produces Aβ peptides, mostly as the soluble Aβ40 with fewer insoluble Aβ42 peptides. Rare, early-onset AD (EOAD) occurs in individuals under 60 years of age. Most EOAD cases are due to unknown genetic causes, but a subset is due to mutations in the genes encoding the amyloid precursor protein that is processed into Aβ peptides or the presenilins (PS1 and PS2) that process APP. PS1 interacts with the epsilon isoform of glial fibrillary acidic protein (GFAPɛ), a protein found in the subventricular zone of the brain. We have found that GFAPɛ interacts with the telomere protection factor RAP1 (TERF2IP). RAP1 can also interact with PS1 alone or with GFAPɛ in vitro. Our data show that the nuclear protein RAP1 has an extratelomeric role in the cytoplasm through its interactions with GFAPɛ and PS1. GFAPɛ coprecipitated with RAP1 from human cell extracts. RAP1, GFAPɛ, and PS1 all colocalized in human SH-SY5Y cells. Using a genetic model of the γ-secretase complex in Saccharomyces cerevisiae, RAP1 increased γ-secretase activity, and this was potentiated by GFAPɛ. Our studies are the first to connect RAP1 with an age-related disorder.
Distilling “Urban Kernel” from the Revival Processes from War Damages in Japanese Local Cities

In 2011, Tohoku Region Pacific Coast Earthquake attacked Japan and the Tsunami destroyed a number of cities completely. After 2 years, the way of revival are discussed right now. In the process, how the community can be reproduced becomes hot issue. The city vanished instantly, therefore, they need to reproduce not only buildings but also lifestyles. However, this is not first experience for Japanese. The war damage revivals were carried out after WWII. The purpose of this study is to investigate the revival processes from war damage in Japanese local cities and reveal the "Urban Kernel" from them. Urban Kernel is an implicit norm to reproduce urban fabric. By using this concept, an alternative viewpoint in city planning would be shown.
SUPPORTING INFORMATION FOR PUBLICATION FOR Femtosecond laser generation of microbumps and nanojets on single and bilayer Cu/Ag thin films

The conversion of absorbed fluence used in the TTM-MD modeling to incident fluence usually specified in the presentation of experimental results is performed based on the results of a series of TTM simulations accounting for the electron temperature dependence of the reflectivity and optical absorption coefficient. The laser parameters such as wavelength and pulse duration, as well as the temperature dependences of electron-phonon coupling coefficient, electron heat capacity, and electron thermal conductivity are the same as in the TTM-MD model described in Methods. The lattice heat capacity of Cu and Ag is taken to be constant and equal to 24.44 J/mol K and 35.35 J/mol K, respectively [1].
Etude comparative de differents modeles mathematiques pour la prediction des niveaux de pollution atmospherique

Prediction a court terme des concentrations de quelques polluants atmospheriques en utilisant un ensemble de donnees experimentales. Deux types d'analyses sont envisagees : l'analyse univariable et l'analyse multivariable. Evaluation de la qualite des differents modeles. Les meilleurs resultats sont obtenus avec le modele arma
RBM14 promotes DNA end resection during homologous recombination repair

DNA double-strand break (DSB) repair by homologous recombination (HR) is crucial for the maintenance of genome stability and integrity. In this study, we aim to identify novel RNA binding proteins (RBPs) involved in HR repair because little is known about RBP function in HR. For this purpose, we carry out pulldown assays using a synthetic ssDNA/dsDNA structure coated with replication protein A (RPA) to mimic resected DNA, a crucial intermediate in HR-mediated DSB repair. Using this approach, we identify RNA-binding motif protein 14 (RBM14) as a potential binding partner. We further show that RBM14 interacts with an essential HR repair factor, CtIP. RBM14 is crucial for CtIP recruitment to DSB sites and for subsequent RPA coating and RAD51 replacement, facilitating efficient HR repair. Moreover, inhibition of RBM14 expression sensitizes cancer cells to X-ray irradiation. Together, our results demonstrate that RBM14 promotes DNA end resection to ensure HR repair and may serve as a potential target for cancer therapy.
Modulation of GaAs nanowire growth by pre-treatment of Si substrate using a Ga focused ion beam

We reveal a novel phenomenon observed after self-catalytic growth of GaAs nanowires (NWs) on Si(111) substrates treated with a Ga focused ion beam (FIB). Depending on the ion dose, NW arrays with various geometrical parameters can be obtained. A minor treatment of the substrate enables a slight increase in the surface density of NWs relative to an unmodified substrate area. As the ion dose is increased up to ∼0.1 pC μm−2, the growth of GaAs NWs and nanocrystals is suppressed. However, a further increase in the ion dose stimulates the crystal growth leading to the formation of extremely thin NWs (39 ± 5 nm) with a remarkably high surface density of up to 15 μm−2. Resting upon an analysis of the surface structure before and after stages of ion-beam treatment, ultra-high vacuum annealing and NW growth, we propose a mechanism underlying the phenomenon observed. We assume that the chemical interaction between embedded Ga ions and a native Si oxide layer leads either to the enhancement of the passivation properties of the oxide layer within FIB-modified areas (at low and middle ion doses), or to the etching of the passivating oxide layer by excess Ga atoms, resulting in the formation of pores (at high ion doses). Due to this behavior, local fabrication of GaAs NW arrays with a diverse range of characteristics can be implemented on the same substrate. This approach opens a new way for self-catalytic growth of GaAs NWs.
Dynamic optimal multi-indexes configuration for estimating the prediction errors of dynamical climate model in North China

Based on the idea of using the historical-analogue information to revise the prediction errors of National Climate Centre numerical business model, for North China, based on analysis data of the CMAP from 1983 to 2009, 40 pieces of climate indices from NOAA, 27 years of the season prediction model results from 1983 to 2009 and 74 pieces of circulation characteristics materials provided by Weather Diagnostic Forecasting Room of National Climate Center, using the method of combining data analysis and numerical simulation of diagnostic tests, taking the advantage of the prediction error of the key information of similar model from the historical data, by identifying key factors, optimizing allocation of the different factors of different forecasting years, we established specific multi-factor dynamic optimal portfolios to revise prediction errors in different periods of the power-statistical model in North China, and constructed early environmental factors similar to field multiple objective criteria, to develop new technology of revising prediction errors from the power-statistical model based on dynamic optimal combination of multi-factor, and improved the prediction effect in the summer precipitation in North China and the forecasting skills. Results of independent sample return of 2005—2009 shows that, the score of similarity revised method has improved significantly compared with the score of systematic revised method. The method has a good prospect for summer precipitation forecast in North China, and is going to be put into operation.
Comparative Efficacy of Tegoprazan vs Esomeprazole/Sodium Bicarbonate for the Treatment of Helicobacter pylori Infection

INTRODUCTION: Potassium-competitive acid blockers and proton pump inhibitors/sodium bicarbonate can rapidly increase intragastric pH. In this study, we aimed to compare the clinical outcomes of tegoprazan-based and esomeprazole/sodium bicarbonate–based triple therapies in the treatment of Helicobacter pylori infection. METHODS: We retrospectively reviewed the data of patients with H. pylori infection treated with a 14-day tegoprazan-based triple therapy or 14-day esomeprazole/sodium bicarbonate–based triple therapy. The primary end point was the H. pylori eradication rate with first-line treatment in an intention-to-treat analysis. Secondary end points included the eradication rate with first-line therapy in the per-protocol analysis and adverse events associated with eradication therapy. RESULTS: Of the 854 included patients, 435 were treated with tegoprazan-based therapy, and 419 received esomeprazole/sodium bicarbonate–based therapy. In the intention-to-treat population, no significant difference in eradication rate was detected between the tegoprazan-treated and esomeprazole/sodium bicarbonate–treated groups (78.6% [95% confidence interval (CI), 74.6–82.3%] vs 81.4% [95% CI, 77.4–84.9%], P = 0.313). The per-protocol analysis also revealed a similar eradication rate between groups (tegoprazan vs esomeprazole/sodium bicarbonate: 85.5% [95% CI, 81.8–87.5%] vs 87.8% [95% CI, 84.1–90.7%], P = 0.339). However, abdominal discomfort and diarrhea were more common in the esomeprazole/sodium bicarbonate–treated group than in the tegoprazan-treated group (abdominal discomfort: 1.1% vs 3.8%, P = 0.012; diarrhea: 9.9% vs 21.2%, P < 0.001). DISCUSSION: The efficacy of the esomeprazole/sodium bicarbonate–based triple therapy for H. pylori eradication was comparable with that of the tegoprazan-based triple therapy. However, esomeprazole/sodium bicarbonate–based therapy exhibited a higher risk of abdominal discomfort and diarrhea than tegoprazan-based therapy.
Exon–intron split analysis reveals posttranscriptional regulatory signals induced by high and low n-6/n-3 polyunsaturated fatty acid ratio diets in piglets

Abstract Polyunsaturated fatty acids (PUFA), such as omega-6 (n-6) and omega-3 (n-3), play a vital role in nutrient metabolism, inflammatory response, and gene regulation. microRNAs (miRNA), which can potentially degrade targeted messenger RNAs (mRNA) and/or inhibit their translation, might play a relevant role in PUFA-related changes in gene expression. Although differential expression analyses can provide a comprehensive picture of gene expression variation, they are unable to disentangle when in the mRNA life cycle the regulation of expression is taking place, including any putative functional miRNA-driven repression. To capture this, we used an exon–intron split analysis (EISA) approach to account for posttranscriptional changes in response to extreme values of n-6/n-3 PUFA ratio. Longissimus dorsi muscle samples of male and female piglets from sows fed with n-6/n-3 PUFA ratio of 13:1 (SOY) or 4:1 (LIN), were analyzed in a bidirectional contrast (LIN vs. SOY, SOY vs. LIN). Our results allowed the identification of genes showing strong posttranscriptional downregulation signals putatively targeted by significantly upregulated miRNA. Moreover, we identified genes primarily involved in the regulation of lipid-related metabolism and immune response, which may be associated with the pro- and anti-inflammatory functions of the n-6 and n-3 PUFA, respectively. EISA allowed us to uncover regulatory networks complementing canonical differential expression analyses, thus providing a more comprehensive view of muscle metabolic changes in response to PUFA concentration.
Fenestrated popliteal vein pierced by a branch of the tibial nerve

Knowledge of anatomical variations is important so as to avoid potential iatrogenic injury or misdiagnosis on imaging. Here we report an unusual finding and relationship between the tibial nerve and popliteal vein. During the routine dissection of an adult cadaver, it was noted that a branch of the tibial nerve in the popliteal fossa pierced the most distal part of the popliteal vein. This unusual finding is described and relevant reports in the literature discussed. Our hopes are that such a report might help surgeons avoid injury to such a fenestrated popliteal vein and the tibial nerve branch traveling through it therefore decreasing patient morbidity.
Participation in a Medicare advanced primary care model and the delivery of high‐value services

Abstract Objective To evaluate whether primary care providers' participation in the Comprehensive Primary Care Plus Initiative (CPC+) was associated with changes in their delivery of high‐value services. Data Sources Medicare Physician & Other Practitioners public use files from 2013 to 2019, 2017 to 2019 Medicare Part B claims for a 5% random sample of Medicare Fee‐for‐Service (FFS) beneficiaries, the Area Health Resources File, the National Plan & Provider Enumeration System files, and public use datasets from the Centers for Medicare & Medicaid Services Physician Compare. Study Design We used a difference‐in‐difference approach with a propensity score‐matched comparison group to estimate the association of CPC+ participation with the delivery of annual wellness visits (AWVs), advance care planning (ACP), flu shots, counseling to prevent tobacco use, and depression screening. These services are prominent examples of high‐value services, providing benefits to patients at a reasonable cost. We examined both the likelihood of delivering these services within a year and the count of services delivered per 1000 Medicare FFS beneficiaries per year. Data Collection/Extraction Methods Secondary data are linked at the provider level. Principal Findings We find that CPC+ participation was associated with increases in the likelihood of delivering AWVs (13.03 percentage points by CPC+'s third year, p < 0.001) and the number of AWVs per 1000 Medicare FFS beneficiaries (44 more AWVs by CPC+'s third year, p < 0.001). We also find that CPC+ participation was associated with more flu shots per 1000 beneficiaries (52 more shots by CPC+'s third year, p < 0.001) but not with the likelihood of delivering flu shots. We did not find consistent evidence for the association between CPC+ participation and ACP services, counseling to prevent tobacco use, or depression screening. Conclusions CPC+ participation was associated with increases in the delivery of AWVs and flu shots, but not other high‐value services.
Representational Similarity Analysis for Tracking Neural Correlates of Haptic Learning on a Multimodal Device

A goal of wearable haptic devices has been to enable haptic communication, where individuals learn to map information typically processed visually or aurally to haptic cues via a process of cross-modal associative learning. Neural correlates have been used to evaluate haptic perception and may provide a more objective approach to assess association performance than more commonly used behavioral measures of performance. In this article, we examine Representational Similarity Analysis (RSA) of electroencephalography (EEG) as a framework to evaluate how the neural representation of multifeatured haptic cues changes with association training. We focus on the first phase of cross-modal associative learning, perception of multimodal cues. A participant learned to map phonemes to multimodal haptic cues, and EEG data were acquired before and after training to create neural representational spaces that were compared to theoretical models. Our perceptual model showed better correlations to the neural representational space before training, while the feature-based model showed better correlations with the post-training data. These results suggest that training may lead to a sharpening of the sensory response to haptic cues. Our results show promise that an EEG-RSA approach can capture a shift in the representational space of cues, as a means to track haptic learning.
Larger presence of ectomycorrhizae detected from pygmy pine ecotype in the fire-frequent pine barrens ecosystem

ABSTRACT Pine barrens ecosystem has acidic, sandy, and nutrient-poor soil and is prone to drought and fire. In the New Jersey Pine Barrens, the predominant pitch pine (Pinus rigida) consists of two ecotypes: the regular pitch pines with heights of 4.6–12 m, and the pygmy pines of low stature (1.2–1.8 m) in the New Jersey Pine Plains. Previous ecological studies suggested that the dwarf pines in the Pine Plains that are embedded within the Pine Barrens were an evolutionary adaptation to frequent fire. Pines are obligate ectomycorrhizal (EcM) mutualists, and their root mycobiota may contribute to stress protection and plant health. However, information on the mycobiota associated with plants in the pine barrens ecosystem is lacking. To have a holistic understanding of the evolution and adaptation in this stressed environment, we used both culture-independent metabarcoding and culture-based method to characterize the mycobiota from soil and root of the two ecotypes and to identify core mycobiota. We found that Agaricomycetes, Leotiomycetes, and Mucoromycotina are predominant fungi in the New Jersey Pine Barrens ecosystem, which is rich in root mutualistic fungi. We observed that the pygmy pine roots had significantly higher density of EcM tips than the regular pine roots. This was corroborated by our metabarcoding analysis, which showed that the pygmy pine trees had higher ratio of ectomycorrhiza-forming fungi than the regular-statured pines. We hypothesize that symbiotrophic EcM fungi associated with pygmy pines are capable of mitigating high fire stress in the Pine Plains.
Restricted mean survival time to estimate an intervention effect in a cluster randomized trial

For time-to-event outcomes, the difference in restricted mean survival time is a measure of the intervention effect, an alternative to the hazard ratio, corresponding to the expected survival duration gain due to the intervention up to a predefined time t*. We extended two existing approaches of restricted mean survival time estimation for independent data to clustered data in the framework of cluster randomized trials: one based on the direct integration of Kaplan-Meier curves and the other based on pseudo-values regression. Then, we conducted a simulation study to assess and compare the statistical performance of the proposed methods, varying the number and size of clusters, the degree of clustering, and the magnitude of the intervention effect under proportional and non-proportional hazards assumption. We found that the extended methods well estimated the variance and controlled the type I error if there was a sufficient number of clusters (≥ 50) under both proportional and non-proportional hazards assumption. For cluster randomized trials with a limited number of clusters (< 50), a permutation test for pseudo-values regression was implemented and corrected the type I error. We also provided a procedure to estimate permutation-based confidence intervals which produced adequate coverage. All the extended methods performed similarly, but the pseudo-values regression offered the possibility to adjust for covariates. Finally, we illustrated each considered method with a cluster randomized trial evaluating the effectiveness of an asthma-control education program.
How has travel behaviour changed since the implementation of the congestion tax in Gothenburg? - A survey study based on individuals living in Gråbo and Särö.

Utslapp fran biltrafik ar kant for att ha en negativ inverkan pa klimatet och manniskors halsa. For att minska utslappen och dess paverkan infordes den forsta januari 2013 en trangselskatt i Goteborg. Skatten belastar dem som reser till och fran Goteborg med bil. Vi har genomfort en enkatundersokning pa individer som bor ungefar 25 kilometer fran Goteborg, for att undersoka hur deras resebeteende har paverkats av trangselskatten. Undersokningen bestod av fragor gallande resmonster med bil och kollektivtrafik, mojliga substitut till bil, attityd mot trangselskatten och socioekonomiska faktorer. Vara resultat visar att i genomsnitt har 22 procent i Grabo, till skillnad mot 16 procent i Saro, minskat sitt bilakande. Motsvarande okning i resande med kollektivtrafik ar 13 procent i Grabo och 5 procent i Saro. Vi har aven hittat tre andra substitut: anpassning av tid och dag for att resan, resa till en annan destination eller att stalla in resan. Dock hittade vi inga andra signifikanta transportsubstitut an kollektivtrafik. Individer med en hogre inkomst paverkas mindre av trangselskatten jamfort med dem som har en lagre inkomst. Aven faktorer som anledning for resa, attityd mot trangselskatten och om en individ har barn har en signifikant paverkan pa forandrat resebeteende efter trangselskattens inforande.
Direct and indirect effects of age on dengue severity: The mediating role of secondary infection

Severe dengue occurrence has been attributed to increasing age and different dengue virus (DENV) serotypes that cause secondary infections and immune-enhancing phenomena. Therefore, we examined if the effect of age on dengue severity was mediated by infectivity status while controlling for sex and region. Further, we assessed the spatial clustering of dengue severity for individuals with primary and secondary infection across Mexican municipalities. Health data from 2012 to 2017 was retrieved from Mexico’s Ministry of Health. A mediation analysis was performed using multiple logistic regression models based on a directed acyclic graph. The models were explored for the direct effect of age on dengue severity and its indirect impact through secondary infection. In addition, severe dengue clusters were determined in some Northeastern and Southeastern municipalities through spatial analysis. We observed a nonlinear trend between age and severe dengue. There was a downward trend of severe dengue for individuals between 0 and 10 years and an upward trend above 10 years. The effect of age on dengue severity was no longer significant for individuals between 10 and 60 years after introducing infectivity status into the model. The mediating role of infectivity status in the causal model was 17%. Clustering of severe dengue among individuals with primary infection in the Northeastern region may point to the high prevalence of DENV-3 in the region. Public health efforts may prevent secondary infection among infants and the aged. In addition, there should be a further investigation into the effect of DENV-3 in individuals with primary disease.