Miracle-dz/UniFAR-FTUs huggingface dataset:
Addressing Prolonged Restore Challenges in Further Scaling DRAMs

As the de facto memory technology, DRAM has enjoyed continuous scaling over the past decades to keep performance growth and capacity enhancement. However, DRAM further scaling into deep sub-micron regime faces significant challenges. Among the induced issues, prolonged restore time is expected to be one of the major concerns, but it has been paid little attention. Aiming at restore issue, this thesis performs pioneering studies to characterize the problems, and presents techniques from different perspectives to overcome them. First, our experimental studies quantify the significant restore process variations, causing serious degradations on yield and/or performance. To solve the problem, we propose schemes to expose the variations to the architectural levels. Fast restore chunks can thus be constructed utilizing DRAM organization, and they can be exposed to the memory controller to effectively compensate the performance loss. Further, we maximize the improvement by applying restore-time-aware rank construction and hotness-aware page allocation schemes to fully utilize the fast regions. Second, in addition to simply expose the variations to higher levels, we investigate DRAM cell structures and behaviors finding that refresh and restore are two strongly correlated operations. Whereas are being fully restored after each read or write access, DRAM cells are always being fully charged by periodical refresh operations, providing an opportunity to early terminate restore. With the insight, we first propose to truncate a restore using the time distance to next refresh. Further, to provide more truncation opportunities, we integrate the multirate-refresh concepts to shorten the distance by increasing the refresh rate of recently accessed regions. Lastly, we explore higher to the application level with the inspiration that a large set of applications can well tolerate output accuracy loss and runtime errors, enabling us to exploit approximate computing to mitigate prolonged restore. By utilizing the variance in restore timing exhibited at different row segments, we reduce the restore time such that only partial segments are fully reliable. We then map the critical data onto the reliable segments to keep the application-level errors low. Atop of the approximation-aware technique, we further generalize it to support precise computing as well.
A deep learning genome-mining strategy for biosynthetic gene cluster prediction

Abstract Natural products represent a rich reservoir of small molecule drug candidates utilized as antimicrobial drugs, anticancer therapies, and immunomodulatory agents. These molecules are microbial secondary metabolites synthesized by co-localized genes termed Biosynthetic Gene Clusters (BGCs). The increase in full microbial genomes and similar resources has led to development of BGC prediction algorithms, although their precision and ability to identify novel BGC classes could be improved. Here we present a deep learning strategy (DeepBGC) that offers reduced false positive rates in BGC identification and an improved ability to extrapolate and identify novel BGC classes compared to existing machine-learning tools. We supplemented this with random forest classifiers that accurately predicted BGC product classes and potential chemical activity. Application of DeepBGC to bacterial genomes uncovered previously undetectable putative BGCs that may code for natural products with novel biologic activities. The improved accuracy and classification ability of DeepBGC represents a major addition to in-silico BGC identification.
Targeting reduced mitochondrial DNA quantity as a therapeutic approach in pediatric high-grade gliomas

Abstract Background Despite increased understanding of the genetic events underlying pediatric high-grade gliomas (pHGGs), therapeutic progress is static, with poor understanding of nongenomic drivers. We therefore investigated the role of alterations in mitochondrial function and developed an effective combination therapy against pHGGs. Methods Mitochondrial DNA (mtDNA) copy number was measured in a cohort of 60 pHGGs. The implication of mtDNA alteration in pHGG tumorigenesis was studied and followed by an efficacy investigation using patient-derived cultures and orthotopic xenografts. Results Average mtDNA content was significantly lower in tumors versus normal brains. Decreasing mtDNA copy number in normal human astrocytes led to a markedly increased tumorigenicity in vivo. Depletion of mtDNA in pHGG cells promoted cell migration and invasion and therapeutic resistance. Shifting glucose metabolism from glycolysis to mitochondrial oxidation with the adenosine monophosphate–activated protein kinase activator AICAR (5-aminoimidazole-4-carboxamide ribonucleotide) or the pyruvate dehydrogenase kinase inhibitor dichloroacetate (DCA) significantly inhibited pHGG viability. Using DCA to shift glucose metabolism to mitochondrial oxidation and then metformin to simultaneously target mitochondrial function disrupted energy homeostasis of tumor cells, increasing DNA damage and apoptosis. The triple combination with radiation therapy, DCA and metformin led to a more potent therapeutic effect in vitro and in vivo. Conclusions Our results suggest metabolic alterations as an onco-requisite factor of pHGG tumorigenesis. Targeting reduced mtDNA quantity represents a promising therapeutic strategy for pHGG.
Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination

Significance Long noncoding RNAs (lncRNAs) are known to be involved in several immunological processes. In spite of their general relevance to human immunity, to date there are no reports on the importance of lncRNAs in vaccine responses. Here we apply a “systems vaccinology” framework to study the role of lncRNAs in vaccine-mediated immunity. We applied meta-analytical approaches using public microarray data from over 2,000 blood transcriptome samples of vaccinees and an RNA-sequencing (RNA-seq) dataset from vaccinated children to tackle this question. Our results indicate that lncRNAs are important players in several immunological processes elicited by vaccination. Understanding the mechanisms of vaccine-elicited protection contributes to the development of new vaccines. The emerging field of systems vaccinology provides detailed information on host responses to vaccination and has been successfully applied to study the molecular mechanisms of several vaccines. Long noncoding RNAs (lncRNAs) are crucially involved in multiple biological processes, but their role in vaccine-induced immunity has not been explored. We performed an analysis of over 2,000 blood transcriptome samples from 17 vaccine cohorts to identify lncRNAs potentially involved with antibody responses to influenza and yellow fever vaccines. We have created an online database where all results from this analysis can be accessed easily. We found that lncRNAs participate in distinct immunological pathways related to vaccine-elicited responses. Among them, we showed that the expression of lncRNA FAM30A was high in B cells and correlates with the expression of immunoglobulin genes located in its genomic vicinity. We also identified altered expression of these lncRNAs in RNA-sequencing (RNA-seq) data from a cohort of children following immunization with intranasal live attenuated influenza vaccine, suggesting a common role across several diverse vaccines. Taken together, these findings provide evidence that lncRNAs have a significant impact on immune responses induced by vaccination.
Calcium-Sensing Receptor Internalization Is β-Arrestin–Dependent and Modulated by Allosteric Ligands

G protein–coupled receptor (GPCR) internalization is crucial for the termination of GPCR activity, and in some cases is associated with G protein–independent signaling and endosomal receptor signaling. To date, internalization has been studied in great detail for class A GPCRs; whereas it is not well established to what extent the observations can be generalized to class C GPCRs, including the extracellular calcium-sensing receptor (CaSR). The CaSR is a prototypical class C GPCR that maintains stable blood calcium (Ca2+) levels by sensing minute changes in extracellular free Ca2+. It is thus necessary that the activity of the CaSR is tightly regulated, even while continuously being exposed to its endogenous agonist. Previous studies have used overexpression of intracellular proteins involved in GPCR trafficking, pathway inhibitors, and cell-surface expression or functional desensitization as indirect measures to investigate CaSR internalization. However, there is no general consensus on the processes involved, and the mechanism of CaSR internalization remains poorly understood. The current study provides new insights into the internalization mechanism of the CaSR. We have used a state-of-the-art time-resolved fluorescence resonance energy transfer–based internalization assay to directly measure CaSR internalization in real-time. We demonstrate that the CaSR displays both constitutive and concentration-dependent Ca2+-mediated internalization. For the first time, we conclusively show that CaSR internalization is sensitive to immediate positive and negative modulation by the CaSR-specific allosteric modulators N-(3-[2-chlorophenyl]propyl)-(R)-α-methyl-3-methoxybenzylamine (NPS R-568) and 2-chloro-6-[(2R)-2-hydroxy-3-[(2-methyl-1-naphthalen-2-ylpropan-2-yl)amino]propoxy]benzonitrile (NPS 2143), respectively. In addition, we provide compelling evidence that CaSR internalization is β-arrestin–dependent while interestingly being largely independent of Gq/11 and Gi/o protein signaling. SIGNIFICANCE STATEMENT A novel highly efficient cell-based real-time internalization assay to show that calcium-sensing receptor (CaSR) internalization is β-arrestin-dependent and sensitive to modulation by allosteric ligands.
Glutathione infusion before primary percutaneous coronary intervention: a randomised controlled pilot study

Objective In the setting of reperfused ST-elevation myocardial infarction (STEMI), increased production of reactive oxygen species (ROS) contributes to reperfusion injury. Among ROS, hydrogen peroxide (H2O2) showed toxic effects on human cardiomyocytes and may induce microcirculatory impairment. Glutathione (GSH) is a water-soluble tripeptide with a potent oxidant scavenging activity. We hypothesised that the infusion of GSH before acute reoxygenation might counteract the deleterious effects of increased H2O2 generation on myocardium. Methods Fifty consecutive patients with STEMI, scheduled to undergo primary angioplasty, were randomly assigned, before intervention, to receive an infusion of GSH (2500 mg/25 mL over 10 min), followed by drug administration at the same doses at 24, 48 and 72 hours elapsing time or placebo. Peripheral blood samples were obtained before and at the end of the procedure, as well as after 5 days. H2O2 production, 8-iso-prostaglandin F2α (PGF2α) formation, H2O2 breakdown activity (HBA) and nitric oxide (NO) bioavailability were determined. Serum cardiactroponin T (cTpT) was measured at admission and up to 5 days. Results Following acute reperfusion, a significant reduction of H2O2 production (p=0.0015) and 8-iso-PGF2α levels (p=0.0003), as well as a significant increase in HBA (p<0.0001)and NO bioavailability (p=0.035), was found in the GSH group as compared with placebo. In treated patients, attenuated production of H2O2 persisted up to 5 days from the index procedure (p=0.009) and these changes was linked to those of the cTpT levels (r=0.41, p=0.023). Conclusion The prophylactic and prolonged infusion of GSH seems to determine a rapid onset and persistent blunting of H2O2 generation improving myocardial cell survival. Nevertheless, a larger trial, adequately powered for evaluation of clinical endpoints, is ongoing to confirm the current finding. Trial registration number EUDRACT 2014-00448625; Pre-results.
Profiling DNA methylation patterns of zebrafish liver associated with parental high dietary arachidonic acid

Diet has been shown to influence epigenetic key players, such as DNA methylation, which can regulate the gene expression potential in both parents and offspring. Diets enriched in omega-6 and deficient in omega-3 PUFAs (low dietary omega-3/omega-6 PUFA ratio), have been associated with the promotion of pathogenesis of diseases in humans and other mammals. In this study, we investigated the impact of increased dietary intake of arachidonic acid (ARA), a physiologically important omega-6 PUFA, on 2 generations of zebrafish. Parental fish were fed either a low or a high ARA diet, while the progeny of both groups were fed the low ARA diet. We screened for DNA methylation on single base-pair resolution using reduced representation bisulfite sequencing (RRBS). The DNA methylation profiling revealed significant differences between the dietary groups in both parents and offspring. The majority of differentially methylated loci associated with high dietary ARA were found in introns and intergenic regions for both generations. Common loci between the identified differentially methylated loci in F0 and F1 livers were reported. We described overlapping gene annotations of identified methylation changes with differential expression, but based on a small number of overlaps. The present study describes the diet-associated methylation profiles across genomic regions, and it demonstrates that parental high dietary ARA modulates DNA methylation patterns in zebrafish liver.
Overactivity or blockade of transforming growth factor‐β each generate a specific ureter malformation

Transforming growth factor‐β (TGFβ) has been reported to be dysregulated in malformed ureters. There exists, however, little information on whether altered TGFβ levels actually perturb ureter development. We therefore hypothesised that TGFβ has functional effects on ureter morphogenesis. Tgfb1, Tgfb2 and Tgfb3 transcripts coding for TGFβ ligands, as well as Tgfbr1 and Tgfbr2 coding for TGFβ receptors, were detected by quantitative polymerase chain reaction in embryonic mouse ureters collected over a wide range of stages. As assessed by in situ hybridisation and immunohistochemistry, the two receptors were detected in embryonic urothelia. Next, TGFβ1 was added to serum‐free cultures of embryonic day 15 mouse ureters. These organs contain immature smooth muscle and urothelial layers and their in vivo potential to grow and acquire peristaltic function can be replicated in serum‐free organ culture. Such organs therefore constitute a suitable developmental stage with which to define roles of factors that affect ureter growth and functional differentiation. Exogenous TGFβ1 inhibited growth of the ureter tube and generated cocoon‐like dysmorphogenesis. RNA sequencing suggested that altered levels of transcripts encoding certain fibroblast growth factors (FGFs) followed exposure to TGFβ. In serum‐free organ culture exogenous FGF10 but not FGF18 abrogated certain dysmorphic effects mediated by exogenous TGFβ1. To assess whether an endogenous TGFβ axis functions in developing ureters, embryonic day 15 explants were exposed to TGFβ receptor chemical blockade; growth of the ureter was enhanced, and aberrant bud‐like structures arose from the urothelial tube. The muscle layer was attenuated around these buds, and peristalsis was compromised. To determine whether TGFβ effects were limited to one stage, explants of mouse embryonic day 13 ureters, more primitive organs, were exposed to exogenous TGFβ1, again generating cocoon‐like structures, and to TGFβ receptor blockade, again generating ectopic buds. As for the mouse studies, immunostaining of normal embryonic human ureters detected TGFβRI and TGFβRII in urothelia. Collectively, these observations reveal unsuspected regulatory roles for endogenous TGFβ in embryonic ureters, fine‐tuning morphogenesis and functional differentiation. Our results also support the hypothesis that the TGFβ up‐regulation reported in ureter malformations impacts on pathobiology. Further experiments are needed to unravel the intracellular signalling mechanisms involved in these dysmorphic responses. © 2019 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
A Qualitative Study on Gendered Barriers to Livestock Vaccine Uptake in Kenya and Uganda and Their Implications on Rift Valley Fever Control

Rift Valley fever (RVF) is a zoonotic disease of great public health and economic importance transmitted by mosquitoes. The main method of preventing the disease is vaccination of susceptible livestock before outbreaks occur. Studies on RVF vaccines have focused on the production processes, safety, and efficacy standards but those on uptake and adoption levels are rare. This study sought to understand the barriers faced by men and women farmers in the uptake of livestock vaccines to inform strategies for optimizing the use of vaccines against RVF in East Africa. The cross-sectional qualitative study utilized the pairwise ranking technique in sex disaggregated focus group discussions to identify and rank these barriers. Results indicate that men and women farmers experience barriers to vaccine uptake differentially. The barriers include the direct and indirect cost of vaccines, distances to vaccination points, availability of vaccination crushes, intra-household decision making processes and availability of information on vaccination campaigns. The study concludes that vaccine provision does not guarantee uptake at the community level. Hence, these barriers should be considered while designing vaccination strategies to enhance community uptake because vaccine uptake is a complex process which requires buy-in from men and women farmers, veterinary departments, county/district and national governments, and vaccine producers.
The Functional Power of the Human Milk Proteome

Human milk is the most complete and ideal form of nutrition for the developing infant. The composition of human milk consistently changes throughout lactation to meet the changing functional needs of the infant. The human milk proteome is an essential milk component consisting of proteins, including enzymes/proteases, glycoproteins, and endogenous peptides. These compounds may contribute to the healthy development in a synergistic way by affecting growth, maturation of the immune system, from innate to adaptive immunity, and the gut. A comprehensive overview of the human milk proteome, covering all of its components, is lacking, even though numerous analyses of human milk proteins have been reported. Such data could substantially aid in our understanding of the functionality of each constituent of the proteome. This review will highlight each of the aforementioned components of human milk and emphasize the functionality of the proteome throughout lactation, including nutrient delivery and enhanced bioavailability of nutrients for growth, cognitive development, immune defense, and gut maturation.
A DNA-Based Biosensor Assay for the Kinetic Characterization of Ion-Dependent Aptamer Folding and Protein Binding

Therapeutic and diagnostic nucleic acid aptamers are designed to bind tightly and specifically to their target. The combination of structural and kinetic analyses of aptamer interactions has gained increasing importance. Here, we present a fluorescence-based switchSENSE aptasensor for the detailed kinetic characterization of aptamer–analyte interaction and aptamer folding, employing the thrombin-binding aptamer (TBA) as a model system. Thrombin-binding aptamer folding into a G-quadruplex and its binding to thrombin strongly depend on the type and concentration of ions present in solution. We observed conformational changes induced by cations in real-time and determined the folding and unfolding kinetics of the aptamer. The aptamer’s affinity for K+ was found to be more than one order of magnitude higher than for other cations (K+ > NH4+ >> Na+ > Li+). The aptamer’s affinity to its protein target thrombin in the presence of different cations followed the same trend but differed by more than three orders of magnitude (KD = 0.15 nM to 250 nM). While the stability (kOFF) of the thrombin–TBA complex was similar in all conditions, the cation type strongly influenced the association rate (kON). These results demonstrated that protein–aptamer binding is intrinsically related to the correct aptamer fold and, hence, to the presence of stabilizing ions. Because fast binding kinetics with on-rates exceeding 108 M−1s−1 can be quantified, and folding-related phenomena can be directly resolved, switchSENSE is a useful analytical tool for in-depth characterization of aptamer–ion and aptamer–protein interactions.
A Comparison of the Impact of Two Methods of Nutrition-Behavioral Intervention on Selected Auxological and Biochemical Parameters in Obese Prepubertal Children—Crossover Preliminary Study

Obese children are exposed to short and long-term health consequences, such as dyslipidemia, hypertension and diabetes mellitus. For these reasons, the prevention and treatment of obesity in the pediatric population is a challenge for health care professionals. The aim of this study was to evaluate whether an intensive intervention based on diet and physical activity has a better impact on the auxological and biochemical parameters than standard care (intervention). The study included 20 children (six boys, 14 girls), of the mean age 8.9 (SD 1.4) before puberty. The participants were randomly assigned to two groups: Group I (starting treatment with intensive intervention), and II (starting treatment with standard intervention). After three months, the groups were switched. The comparison of the two interventions in the study group indicates a better effectiveness of intensive intervention in the improvement of anthropometric parameters and majority of biochemical ones (except for insulin concentration, HOMA IR index and LDL cholesterol). As the result of intensive intervention, the mean % of weight-to-height excess and hip circumference decreased significantly (p < 0.005). Our results confirm that complex intervention based on systematic control visits, including personalized dietitian counselling and physician care, during the weight reduction process is more effective than a one-off standard visit.
EMT and Stemness—Key Players in Pancreatic Cancer Stem Cells

Metastasis and tumor progression are the major cause of death in patients suffering from pancreatic ductal adenocarcinoma. Tumor growth and especially dissemination are typically associated with activation of an epithelial-to-mesenchymal transition (EMT) program. This phenotypic transition from an epithelial to a mesenchymal state promotes migration and survival both during development and in cancer progression. When re-activated in pathological contexts such as cancer, this type of developmental process confers additional stemness properties to specific subsets of cells. Cancer stem cells (CSCs) are a subpopulation of cancer cells with stem-like features that are responsible for the propagation of the tumor as well as therapy resistance and cancer relapse, but also for circulating tumor cell release and metastasis. In support of this concept, EMT transcription factors generate cells with stem cell properties and mediate chemoresistance. However, their role in pancreatic ductal adenocarcinoma metastasis remains controversial. As such, a better characterization of CSC populations will be crucial in future development of therapies targeting these cells. In this review, we will discuss the latest updates on the mechanisms common to pancreas development and CSC-mediated tumor progression.