Miracle-dz/UniFAR-FTUs huggingface dataset:
Prohibitin: A Novel Molecular Player in KDEL Receptor Signalling

The KDEL receptor (KDELR) is a seven-transmembrane-domain protein involved in retrograde transport of protein chaperones from the Golgi complex to the endoplasmic reticulum. Our recent findings have shown that the Golgi-localised KDELR acts as a functional G-protein-coupled receptor by binding to and activating Gs and Gq. These G proteins induce activation of PKA and Src and regulate retrograde and anterograde Golgi trafficking. Here we used an integrated coimmunoprecipitation and mass spectrometry approach to identify prohibitin-1 (PHB) as a KDELR interactor. PHB is a multifunctional protein that is involved in signal transduction, cell-cycle control, and stabilisation of mitochondrial proteins. We provide evidence that depletion of PHB induces intense membrane-trafficking activity at the ER–Golgi interface, as revealed by formation of GM130-positive Golgi tubules, and recruitment of p115, β-COP, and GBF1 to the Golgi complex. There is also massive recruitment of SEC31 to endoplasmic-reticulum exit sites. Furthermore, absence of PHB decreases the levels of the Golgi-localised KDELR, thus preventing KDELR-dependent activation of Golgi-Src and inhibiting Golgi-to-plasma-membrane transport of VSVG. We propose a model whereby in analogy to previous findings (e.g., the RAS-RAF signalling pathway), PHB can act as a signalling scaffold protein to assist in KDELR-dependent Src activation.
Inhibition of Ep3 attenuates migration and promotes apoptosis of non-small cell lung cancer cells via suppression of TGF-β/Smad signaling

Non-small cell lung cancer (NSCLC) is the most common cause of cancer-associated mortality worldwide. Prostaglandin E2 (PGE2) regulates various biological processes, including invasion, proliferation and apoptosis. E-prostanoid 3 (Ep3) is a PGE2 receptor, and the functional role of Ep3 in the progression of NSCLC remains unresolved. The present study investigated the effects of Ep3 in A549 cells and explored the underlying molecular mechanisms. The results revealed that the mRNA and protein expression levels of Ep3 were significantly upregulated in NSCLC tissues and A549 cells. Pharmacological inhibition of Ep3 or RNA interference against Ep3 attenuated the cell viability, migration and invasion, and promoted apoptosis in A549 cells. Ep3 deficiency also decreased the expression of transforming growth factor (TGF)-β, phosphorylated (p)-Smad2 and p-Smad3. The transfection of TGF-β overexpression plasmids reversed the effects of Ep3 deficiency on the cell viability and apoptosis in A549 cells. Finally, an in vivo experiment revealed that Ep3-siRNA transfection strongly reduced the tumor growth and tumor volume. The Ep3-siRNA transfection also inhibited tumor metastasis via suppression of the expression of metastasis-associated proteins. Taken together, these findings indicate that inhibition of Ep3 attenuates the viability and migration, and promotes the apoptosis of NSCLC through suppression of the TGF-β/Smad signaling pathway. Targeting of the Ep3/TGF-β/Smad signaling pathway may be a novel therapeutic strategy for the prevention and treatment of NSCLC.
Clinical Outcomes for Gastric Cancer following Adjuvant Chemoradiation Utilizing Intensity Modulated versus Three-Dimensional Conformal Radiotherapy

Purpose/Objective(s) To determine if intensity modulated radiation therapy (IMRT) in the post-operative setting for gastric cancer was associated with reduced toxicity compared to 3D conformal radiation therapy (3DCRT). Materials/Methods This retrospective study includes 24 patients with stage IB-IIIB gastric cancer consecutively treated from 2001–2010. All underwent surgery followed by adjuvant chemoradiation. Concurrent chemotherapy consisted of 5-FU/leucovorin (n = 21), epirubicin/cisplatin/5FU (n = 1), or none (n = 2). IMRT was utilized in 12 patients and 3DCRT in 12 patients. For both groups, the target volume included the tumor bed, anastomosis, gastric stump, and regional lymphatics. Results Median follow-up for the entire cohort was 19 months (range 0.4–8.5 years), and 49 months (0.5–8.5 years) in surviving patients. The 3DCRT group received a median dose of 45 Gy, and the IMRT group received a median dose of 50.4 Gy (p = 0.0004). For the entire cohort, 3-year overall survival (OS) was 40% and 3-year disease free survival (DFS) was 41%. OS and DFS did not differ significantly between the groups. Acute toxicity was similar. Between 3DCRT and IMRT groups, during radiotherapy, median weight lost (3.2 vs. 3.3 kg, respectively; p = 0.47) and median percent weight loss were similar (5.0% vs. 4.3%, respectively; p = 0.43). Acute grade 2 toxicity was experienced by 8 patients receiving 3DCRT and 11 receiving IMRT (p = 0.32); acute grade 3 toxicity occurred in 1 patient receiving 3DCRT and none receiving IMRT (p = 1.0). No patients in either cohort experienced late grade 3 toxicity, including renal or gastrointestinal toxicity. At last follow up, the median increase in creatinine was 0.1 mg/dL in the IMRT group and 0.1 mg/dL in the 3DCRT group (p = 0.78). Conclusion This study demonstrates that adjuvant chemoradiation for gastric cancer with IMRT to 50.4 Gy was well-tolerated and compared similarly in toxicity with 3DCRT to 45 Gy.
Derivation of Corneal Endothelial Cell-Like Cells from Rat Neural Crest Cells In Vitro

The aim of this study was to investigate the feasibility of inducing rat neural crest cells (NCC) to differentiate to functional corneal endothelial cell (CEC)-like cells in vitro. Rat NCC were induced with adult CEC-derived conditioned medium. Immunofluorescence, flow cytometry and real time RT-PCR assay were used to detect expression of the corneal endothelium differentiation marker N-cadherin and transcription factors FoxC1 and Pitx2. CFDA SE-labeled CEC-like cells were transplanted to the corneal endothelium of a rat corneal endothelium deficiency model, and an eye-down position was maintained for 24 hours to allow cell attachment. The animals were observed for as long as 2 months after surgery and underwent clinical and histological examination. Spindle-like NCC turned to polygonal CEC-like after induction and expressed N-cadherin, FoxC1, Pitx2, zonula occludens-1 and sodium-potassium pump Na+/K+ ATPase. The corneas of the experimental group were much clearer than those of the control group and the mean corneal thickness in the experimental group was significantly less than in the control group7, 14, 21 and 28 days after surgery. Confocal microscopy through focusing and histological analysis confirmed that green fluorescence-positive CEC-like cells formed a monolayer covering the Descemet’s membrane in the experimental group. In conclusion, CEC-like cells derived from NCCs displayed characters of native CEC, and the induction protocol provides guidance for future human CEC induction from NCC.
Data Centric Storage Technologies: Analysis and Enhancement

This paper surveys the most relevant works of Data Centric Storage (DCS) for Wireless Sensor Networks. DCS is a research area that covers data dissemination and storage inside an ad-hoc sensor network. In addition, we present a Quadratic Adaptive Replication (QAR) scheme for DCS, which is a more adaptive multi-replication DCS system and outperforms previous proposals in the literature by reducing the overall network traffic that has a direct impact on energy consumption. Finally, we discuss the open research challenges for DCS.
Heritability of risk factors for primary open-angle glaucoma: the Beaver Dam Eye Study.

PURPOSE To investigate the family aggregation and heritability of risk indicators of primary open-angle glaucoma. METHODS During the baseline examination of the Beaver Dam Eye Study, standardized measurements of intraocular pressure were performed with a Goldmann applanation tonometer. Stereoscopic photographs of the optic discs were taken of both eyes of each study participant. The eyes were graded for the size of the optic disc and cup according to a standardized protocol, with graders masked to other subject characteristics. Family members who had participated in the examination phase were identified. RESULTS Correlations in sibling pairs (n = 1136), parent-child pairs (n = 514), and cousin pairs (n = 1807) for intraocular pressure were 0.17, 0.18, and 0.12, respectively and were all statistically significant, whereas the spouse pair correlation was not. Correlations for sibling, parent-child, and avuncular pairs were higher for vertical optic disc, vertical optic cup, and vertical cup-to-disc ratio than for intraocular pressure. Heritability estimates were 0.36, 0.55, 0.57, and 0.48 for intraocular pressure, optic cup diameter, optic disc diameter, and cup-to-disc ratio, respectively. Correlations for the optic disc parameters were compatible with the amount of gene sharing in relative pairs of different degrees. CONCLUSIONS Risk indicators of open-angle glaucoma correlate highly in families, and the patterns are consistent with the hypothesis of genetic determinants of these factors.
Correlation Hashing Network for Efficient Cross-Modal Retrieval

Hashing is widely applied to approximate nearest neighbor search for large-scale multimodal retrieval with storage and computation efficiency. Cross-modal hashing improves the quality of hash coding by exploiting semantic correlations across different modalities. Existing cross-modal hashing methods first transform data into low-dimensional feature vectors, and then generate binary codes by another separate quantization step. However, suboptimal hash codes may be generated since the quantization error is not explicitly minimized and the feature representation is not jointly optimized with the binary codes. This paper presents a Correlation Hashing Network (CHN) approach to cross-modal hashing, which jointly learns good data representation tailored to hash coding and formally controls the quantization error. The proposed CHN is a hybrid deep architecture that constitutes a convolutional neural network for learning good image representations, a multilayer perception for learning good text representations, two hashing layers for generating compact binary codes, and a structured max-margin loss that integrates all things together to enable learning similarity-preserving and high-quality hash codes. Extensive empirical study shows that CHN yields state of the art cross-modal retrieval performance on standard benchmarks.
The Effects of Visual Distracter Complexity on Auditory Evoked P3b in Contact Sports Athletes

“Classic” P3b auditory oddball paradigms are insensitive to subtle deficits. An auditory oddball paradigm paired with visual distracters was used to compare football players with history of concussion, football players without history of concussion, and non-contact sport athletes. As hypothesized, increasing complexity of, and attention to, visual distracters reduced P3b amplitude. P3b amplitudes from non-contact athletes were larger than those from football players; however, players with and without a history of concussion were not significantly different. An auditory oddball paradigm with simple visual distracter improves sensitivity to cognitive deficits. Subconcussive impacts may contribute to brain damage frequently attributed to concussions.
A Cross-Layer Framework for Exploiting Virtual MISO Links in Mobile Ad Hoc Networks

Space-time communications can help combat fading and, hence, can significantly increase the capacity of ad hoc networks. Cooperative diversity or virtual antenna arrays facilitate spatio-temporal communications without actually requiring the deployment of physical antenna arrays. Virtual MISO entails the simultaneous transmission of appropriately encoded information by multiple nodes to effectively emulate a transmission on an antenna array. We present a novel multilayer approach for exploiting virtual MISO links in ad hoc networks. The approach spans the physical, medium access control and routing layers, and provides 1) a significant improvement in the end-to-end performance in terms of throughput and delay and 2) robustness to mobility and interference-induced link failures. The key physical layer property that we exploit is an increased transmission range due to achieved diversity gain. Except for space-time signal processing capabilities, our design does not require any additional hardware. We perform extensive simulations to quantify the benefits of our approach using virtual MISO links. As compared to using only SISO links, we achieve an increase of up to 150 percent in terms of the end-to-end throughput and a decrease of up to 75 percent in the incurred end-to-end delay. Our results also demonstrate a reduction in the route discovery attempts due to link failures by up to 60 percent, a direct consequence of the robustness that our approach provides to link failures
Supplementary Results

Generation of core-orthologs: InParanoid-TC For this study we compute orthologs for each pair of primer-taxa with InParanoid. The pair-wise orthology predictions are subsequently extended to include all primer-taxa by using a criterion of transitive closure (InParanoid-TC). This approach has the advantage of generating ortholog clusters, with only one sequence per taxon. Such clusters can then be directly used for downstream standard approaches of phylogeny reconstruction. In brief, we order the n primer-taxa such that taxon i+1 is the closest relative to taxon i in the species tree, for i = 1, 2, . , n-1, where ties are broken randomly. For each protein in taxon 1 we carry out the following loop: a) We identify the corresponding InParanoid-orthologs in taxon 2. If more than one co-ortholog exists, we choose the one with the highest InParanoid-score. b) With the protein from taxon 2 we identify the ortholog with the highest InParanoid-score in taxon 3. This procedure continues until the ortholog-pair for taxon n-1 and n has been determined. c) The circle is then closed, by identifying the ortholog to the protein from taxon n in taxon 1. d) If the two proteins in taxon 1 at the beginning and the end of the round trip are identical, we keep the set of orthologs and call it core-ortholog. Else, we discard the proteins. We end up with a collection of core-orthologs representing genes present in all primer-taxa. In each individual core-ortholog each taxon is represented exactly once.
The Potential of Bio-drying Process in Improving Quality of the Processed Waste from the Mechanical Biological Treatment for Industrial Heating Systems

This research has an objective to improve quality of theprocessed waste from the mechanical biological treatment (MBT) by using bio-drying process. The processed waste has high moisture content and low heating value because municipality solid waste (MSW), a major source of the waste, lacks of proper waste segregation. These properties make the processed waste not suitable for being used as refuse-derived fuel in waste-to-energy generation and industrial heating systems. Bio-drying is the process that utilizes aerobic decomposition of microbes such as bacteria and fungi on biomass content of the processed waste. We studied effects of operational parameters such as temperature, humidity and heating value of the processed waste before and after applying the bio-drying process. High-quality RDF should have minimum heating value of 5,000 kcal/kg and maximum moisture content of 30%. We found that the processed waste before applying the bio-drying process has the lower heating value (LHV) of 2,451 kcal/kg and moisture content of 53%, while after applying the bio-drying process, with airflow rate of 840 m2/hour every 3 hours for 20 days in a closed system, has the LHV of 9,047 kcal/kg and moisture content of 5%. The power used in these experiments was equivalent to electricity charge of 351 THB, while the revenue generated from selling the processed waste as RDF for waste-to-power generation is 750 THB/ton. Summarily, the bio-drying process can improve the quality of the processed waste with low power consumption within a short period of time. The bio-drying process is a solution for tackling waste management crisis and global warming by providing sustainable waste management model for the future.
A general theory of discrete lteringfor LES in complex geometryBy

1. Motivation and objectives In large eddy simulation (LES) of turbulent ows, the dynamics of the large scale structures are computed while the eeect of the small scale turbulence is modeled using a subgrid scale model. The diierential equations describing the space-time evolution of the large scale structures are obtained from the Navier-Stokes equations by applying a low-pass lter. In order for the resulting LES equations to have the same structure as the Navier-Stokes equations, the diierentiation and ltering operations must commute. In inhomogeneous turbulent ows, the minimum size of eddies that need to be resolved is diierent in diierent regions of the ow. Thus the ltering operation should be performed with a variable lter width. In general, ltering and diierentiation do not commute when the lter width is non-uniform in space. The problem of non-commutation of diierentiation and ltering with non-uniform lter widths was studied by Ghosal and Moin (1995), who proposed a new class of lters for which the commutation error could be obtained in closed form. The application of this lter to the Navier-Stokes equations introduces additional terms (due to commutation error) which are of second order in the lter width. Ghosal and Moin suggested that the leading correction term be retained if high order numerical schemes are used to discretize the LES equations. This procedure involves additional numerical complexities which can be avoided by using the lters described in this report. Van der Ven (1995) constructed a family of lters which commute with diierentiation up to any given order in the lter width; however, this approach is limited to a speciic choice of lters and does not address the issue of additional boundary terms that would arise in nite domains. Due to the lack of a straightforward and robust ltering procedure for inhomo-geneous ows, most large eddy simulations performed to date have not made use of explicit lters. The nearly universal approach for LES in complex geometries is to argue that the nite support of the computational mesh together with the low-pass characteristics of the discrete diierencing operators eeectively act as a lter. This procedure will be referred to as implicit ltering since an explicit ltering operation never appears in the solution procedure. Although the technique of implicit lter-ing has been used extensively in the past, there are several compelling reasons to adopt a more systematic approach. Foremost of these is the issue of consistency. While …
Where is the child's environment? A group socialization theory of development.

Do parents have any important long-term effects on the development of their child's personality? This article examines the evidence and concludes that the answer is no. A new theory of development is proposed: that socialization is context-specific and that outside-the-home socialization takes place in the peer groups of childhood and adolescence. Intraand intergroup processes, not dyadic relationships, are responsible for the transmission of culture and for environmental modification of children's personality characteristics. The universality of children's groups explains why development is not derailed by the wide variations in parental behavior found within and between societies.
On the cooccurrence of wintertime temperature anomalies over eastern Asia and eastern North America

The cooccurrence of wintertime temperature anomalies over eastern Asia and eastern North America is examined. The winter days during 1948–2014 are assigned to nine regimes by applying the self‐organizing map clustering method to the area‐averaged land surface temperature anomalies over these two regions. About half of the winter days are associated with concurrent temperature anomalies. The occurrence of the concurrent/nonconcurrent regimes is closely related to the large‐scale circulation conditions. The Eurasian teleconnection pattern and the Pacific‐North American teleconnection pattern are two dominant large‐scale circulation modes associated with the cooccurrence of the temperature anomalies, through their impacts on the intensities of the corresponding troughs. The precursor analysis reveals that the lead time of the early signals for the concurrent cold anomalies is about 4 days longer than that for the concurrent warm anomalies. In addition, the average lead time of the precursor signals for the wintertime temperature anomalies over eastern Asia is longer than that over eastern North America.
Weight Change in Diabetes and Glycemic and Blood Pressure Control

OBJECTIVE—Weight loss in type 2 diabetes is undisputedly important, and data from community settings are limited. We evaluated weight change and resulting glycemic and blood pressure control in type 2 diabetic patients at an HMO. RESEARCH DESIGN AND METHODS—Using electronic medical records, this retrospective cohort study identified 2,574 patients aged 21–75 years who received a new diagnosis of type 2 diabetes between 1997 and 2002. We estimated 3-year weight trajectories using growth curve analyses, grouped similar trajectories into four categories using cluster analysis, compared category characteristics, and predicted year-4 above-goal A1C and blood pressure by group. RESULTS—The weight-trajectory groups were defined as higher stable weight (n = 418; 16.2%), lower stable weight (n = 1,542; 59.9%), weight gain (n = 300; 11.7%), and weight loss (n = 314; 12.2%). The latter had a mean weight loss of 10.7 kg (−9.8%; P < 0.001) by 18 months, with near-complete regain by 36 months. After adjusting for age, sex, baseline control, and related medication use, those with higher stable weight, lower stable weight, or weight-gain patterns were more likely than those who lost weight to have above-goal A1C (odds ratio [OR] 1.66 [95% CI 1.12–2.47], 1.52 [1.08–2.14], and 1.77 [1.15–2.72], respectively). Those with higher stable weight or weight-gain patterns were more likely than those who lost weight to have above-goal blood pressure (1.83 [1.31–2.57] and 1.47 [1.03–2.10], respectively). CONCLUSIONS—A weight-loss pattern after new diagnosis of type 2 diabetes predicted improved glycemic and blood pressure control despite weight regain. The initial period postdiagnosis may be a critical time to apply weight-loss treatments to improve risk factor control.