Miracle-dz/UniFAR-FTUs huggingface dataset:
Implicit Convex Regularizers of CNN Architectures: Convex Optimization of Two- and Three-Layer Networks in Polynomial Time

We study training of Convolutional Neural Networks (CNNs) with ReLU activations and introduce exact convex optimization formulations with a polynomial complexity with respect to the number of data samples, the number of neurons, and data dimension. More specifically, we develop a convex analytic framework utilizing semi-infinite duality to obtain equivalent convex optimization problems for several two- and three-layer CNN architectures. We first prove that two-layer CNNs can be globally optimized via an $\ell_2$ norm regularized convex program. We then show that three-layer CNN training problems are equivalent to an $\ell_1$ regularized convex program that encourages sparsity in the spectral domain. We also extend these results to multi-layer CNN architectures including three-layer networks with two ReLU layers and deeper circular convolutions with a single ReLU layer. Furthermore, we present extensions of our approach to different pooling methods, which elucidates the implicit architectural bias as convex regularizers.
Binding Mechanism Elucidation of the Acute Respiratory Disease Causing Agent Adenovirus of Serotype 7 to Desmoglein-2

The study of viruses causing acute respiratory distress syndromes (ARDS) is more essential than ever at a time when a virus can create a global pandemic in a matter of weeks. Among human adenoviruses, adenovirus of serotype 7 (HAdV7) is one of the most virulent serotypes. This virus regularly re-emerges in Asia and has just been the cause of several deaths in the United States. A critical step of the virus life cycle is the attachment of the knob domain of the fiber (HAd7K) to the cellular receptor desmoglein-2 (DSG2). Complexes between the fiber knob and two extracellular domains of DSG2 have been produced. Their characterization by biochemical and biophysical methods show that these two domains are sufficient for the interaction and that the trimeric HAd7K could accommodate up to three DSG2 receptor molecules. The cryo-electron microscopy (cryo-EM) structure of these complexes at 3.1 Å resolution confirmed the biochemical data, and allowed the identification of the critical amino acid residues for this interaction, which shows similarities with other DSG2 interacting adenoviruses, despite a low homology in the primary sequences.
Virus recovery by tangential flow filtration: A model to guide the design of a sample concentration process

A simple model is developed to describe the instantaneous (rv) and cumulative (Rv) recovery of viruses from water during sample concentration by tangential flow filtration in the regime of constant water recovery, r. A figure of merit, M = rvr, is proposed as an aggregate performance metric that captures both the efficiency of virus recovery and the speed of sample concentration. We derive an expression for virus concentration in the sample as a function of filtration time with the rate‐normalized virus loss, η=1−rvr , as a parameter. A practically relevant case is considered when the rate of virus loss is proportional to the permeation‐driven mass flux of viruses to the membrane: dmaddt∼QpCf≫QpCp . In this scenario, the instantaneous recovery is constant, the cumulative recovery is decreasing as a power function of time, Rv=1−QpV0tη , η mediates the trade‐off between r and rv, and M is maximized at r=ropt=12η . The proposed model can guide the design of the sample concentration process and serve as a framework for quantification and interlaboratory comparison of experimental data on virus recovery.
Interpretable Approach in the Classification of Sequences of Legal Texts

Machine learning applications in the legal field are numerous and diverse. In order to make contribution to both the machine learning community and the legal community, we have made efforts to create a model compatible with the classification of text sequences, valuing the interpretability of the results. The purpose of this paper is to classify Brazilian legal proceedings in three possible status classes, which are (i) archived proceedings, (ii) active proceedings and (iii) suspended proceedings. Although working with portuguese NLP, which can be hard due to lack of resources, our approach performed remarkably well in the classification task. Furthermore, we were able to extract and interpret the patterns learnt by the neural network besides quantifying how those patterns relate to the classification task.
Non-Alcoholic Fatty Liver Disease Markers Associated with Fasting Serum Insulin and Urinary Albumin Excretion Independent of Fasting Plasma Glucose

Objective: We examined the association between non-alcoholic fatty liver disease (NAFLD) markers and fasting serum immunoreactive insulin (FIRI) and urinary albumin excretion (UAE). Subjects and methods: This study comprised Periods I and II from January 2007 to May 2009, and from June 2009 to December 2011, respectively. After excluding people with ethanol intake ≥210 g/week in men and ≥140 g/week in women, 961 people (613 men, 348 women; mean age: 44 years) were included. We evaluated the fatty liver using ultrasonography score (FLUS) and measured liver enzymes. Results: The mean observation period was 25 ± 9 months. We stratified people into two groups by fasting plasma glucose (FPG) in Period I. The cutoff point between the lower FPG and higher FPG was 100 mg/dL. In regression analysis, serum alanine aminotransferase (ALT) (p < 0.001), FLUS (p < 0.001) and γ-glutamyl transpeptidase (GGTP) (p = 0.022) in Period I were independently associated with FIRI in Period II, whereas in all participants FPG was not. ALT (p < 0.001) and GGTP (p = 0.001) were also independently associated with UAE in people with FPG < 100 mg/dL in Period II. Conclusions: Some NAFLD markers were associated with FIRI and UAE independently of fasting plasma glucose.
Phagocytic receptor signaling regulates clathrin and epsin-mediated cytoskeletal remodeling during apoptotic cell engulfment in C. elegans

The engulfment and subsequent degradation of apoptotic cells by phagocytes is an evolutionarily conserved process that efficiently removes dying cells from animal bodies during development. Here, we report that clathrin heavy chain (CHC-1), a membrane coat protein well known for its role in receptor-mediated endocytosis, and its adaptor epsin (EPN-1) play crucial roles in removing apoptotic cells in Caenorhabditis elegans. Inactivating epn-1 or chc-1 disrupts engulfment by impairing actin polymerization. This defect is partially suppressed by inactivating UNC-60, a cofilin ortholog and actin server/depolymerization protein, further indicating that EPN-1 and CHC-1 regulate actin assembly during pseudopod extension. CHC-1 is enriched on extending pseudopods together with EPN-1, in an EPN-1-dependent manner. Epistasis analysis places epn-1 and chc-1 in the same cell-corpse engulfment pathway as ced-1, ced-6 and dyn-1. CED-1 signaling is necessary for the pseudopod enrichment of EPN-1 and CHC-1. CED-1, CED-6 and DYN-1, like EPN-1 and CHC-1, are essential for the assembly and stability of F-actin underneath pseudopods. We propose that in response to CED-1 signaling, CHC-1 is recruited to the phagocytic cup through EPN-1 and acts as a scaffold protein to organize actin remodeling. Our work reveals novel roles of clathrin and epsin in apoptotic-cell internalization, suggests a Hip1/R-independent mechanism linking clathrin to actin assembly, and ties the CED-1 pathway to cytoskeleton remodeling.
Alternative Splicing Regulation of an Alzheimer’s Risk Variant in CLU

Clusterin (CLU) is one of the risk genes most associated with late onset Alzheimer’s disease (AD), and several genetic variants in CLU are associated with AD risk. However, the functional role of known AD risk genetic variants in CLU has been little explored. We investigated the effect of an AD risk variant (rs7982) in the 5th exon of CLU on alternative splicing by using an integrative approach of brain-tissue-based RNA-Seq and whole genome sequencing data from Accelerating Medicines Partnership—Alzheimer’s Disease (AMP-AD). RNA-Seq data were generated from three regions in the temporal lobe of the brain—the temporal cortex, superior temporal gyrus, and parahippocampal gyrus. The rs7982 was significantly associated with intron retention (IR) of the 5th exon of CLU; as the number of alternative alleles (G) increased, the IR rates decreased more significantly in females than in males. Our results suggest a sex-dependent role of rs7982 in AD pathogenesis via splicing regulation.
Influence of foliar application of algae extract and amino acids mixture on fenugreek plants in sandy and clay soils

Abstract. Tarraf SA, Talaat IM, El-Sayed AEB, Balbaa LK. 2015. Influence of foliar application of algae extract and amino acids mixture on fenugreek plants in sandy and clay soils. Nusantara Bioscience 7: 33-37. Two pot experiments were conducted to study the effect of foliar application of algae extract and amino acids mixture on the growth and chemical constituents of fenugreek plants (Trigonella foenum-graecum L.). Plants were sprayed with different concentrations of algae extract (0.0, 2.5, 5.0 g/L) or equivalent of amino acids mixture (0.0, 0.625, 1.25 g/L). The results indicated that foliar application of amino acids mixture enhanced the vegetative growth of fenugreek plants, especially when plants were sprayed with 1.25 g/L amino acids mixture. Data also show that total nitrogen, essential oil percentage, and yield followed the same trend. These results hold true for plants cultivated in either clay soil or sandy soil. Data also indicated that foliar application of algae extract to fenugreek plants significantly increased plant height, number of leaves, number of branches and fresh and dry weights of plant at vegetative growth stage and flowering stage of fenugreek plant, especially in plants treated with 5 g/L algae extract in sandy and clay soils, respectively. Treatment of fenugreek plants with algae extract markedly increased nitrogen, phosphorous and potassium contents, especially at 5 g/L.
Iron Availability Modulates the Response of Endosymbiotic Dinoflagellates to Heat Stress

Warming and nutrient limitation are stressors known to weaken the health of microalgae. In situations of stress, access to energy reserves can minimize physiological damage. Because of its widespread requirements in biochemical processes, iron is an important trace metal, especially for photosynthetic organisms. Lowered iron availability in oceans experiencing rising temperatures may contribute to the thermal sensitivity of reef‐building corals, which rely on mutualisms with dinoflagellates to survive. To test the influence of iron concentration on thermal sensitivity, the physiological responses of cultured symbiotic dinoflagellates (genus Breviolum; family Symbiodiniaceae) were evaluated when exposed to increasing temperatures (26 to 30°C) and iron concentrations ranging from replete (500 pM Fe’) to limiting (50 pM Fe’) under a diurnal light cycle with saturating radiance. Declines in photosynthetic efficiency at elevated temperatures indicated sensitivity to heat stress. Furthermore, five times the amount of iron was needed to reach exponential growth during heat stress (50 pM Fe′ at 26–28°C vs. 250 pM Fe′ at 30°C). In treatments where exponential growth was reached, Breviolum psygmophilum grew faster than B.minutum, possibly due to greater cellular contents of iron and other trace metals. The metal composition of B.psygmophilum shifted only at the highest temperature (30°C), whereas changes in B.minutum were observed at lower temperatures (28°C). The influence of iron availability in modulating each alga’s response to thermal stress suggests the importance of trace metals to the health of coral‐algal mutualisms. Ultimately, a greater ability to acquire scarce metals may improve the tolerance of corals to physiological stressors and contribute to the differences in performance associated with hosting one symbiont species over another.
The Old and the New: Prospects for Non-Integrating Lentiviral Vector Technology

Lentiviral vectors have been developed and used in multiple gene and cell therapy applications. One of their main advantages over other vectors is the ability to integrate the genetic material into the genome of the host. However, this can also be a disadvantage as it may lead to insertional mutagenesis. To address this, non-integrating lentiviral vectors (NILVs) were developed. To generate NILVs, it is possible to introduce mutations in the viral enzyme integrase and/or mutations on the viral DNA recognised by integrase (the attachment sites). NILVs are able to stably express transgenes from episomal DNA in non-dividing cells or transiently if the target cells divide. It has been shown that these vectors are able to transduce multiple cell types and tissues. These characteristics make NILVs ideal vectors to use in vaccination and immunotherapies, among other applications. They also open future prospects for NILVs as tools for the delivery of CRISPR/Cas9 components, a recent revolutionary technology now widely used for gene editing and repair.
Consideration of Migraines Among Risk Factors for Postoperative Nausea and Vomiting

The impact of migraine on postoperative nausea and vomiting (PONV) is controversial, and few studies have focused on their relationship. Thus, we investigated the impact of migraine, among other risk factors, on PONV in a large retrospective study. We analyzed 10 years of clinical data from the Smart Clinical Data Warehouse of Hallym University Medical Center. PONV was defined as nausea or vomiting within the first 24 h after surgery. Patients diagnosed by a neurologist and with a history of triptan use before surgery were enrolled into the migraine group. We enrolled 208,029 patients aged > 18 years who underwent general anesthesia (GA), among whom 19,786 developed PONV within 24 h after GA and 1982 had migraine. Before propensity score matching, the unadjusted and fully adjusted odds ratios (ORs) for PONV in subjects with versus without migraine were 1.52 (95% confidence interval (CI), 1.34–1.72; p < 0.001) and 1.37 (95% CI, 1.21–1.56; p < 0.001), respectively. The OR for PONV in patients with migraine was also high (OR, 1.37; 95% CI, 1.13–1.66; p = 0.001) after matching. Our findings suggest that migraine is a significant risk factor for PONV.
A bacterial size law revealed by a coarse-grained model of cell physiology

Microbial cells are able to reach balanced exponential growth in a variety of environmental conditions. At the single-cell level, this implies coordination between the processes governing cellular growth, cell division and gene expression. A fundamental goal of microbiology is to build a quantitative and predictive understanding of how such coordination is achieved. It is known since long that the size of E. coli cells grown in media of different nutrient quality increases with growth rate. Recent data, however, shows that this relationship is of another nature when growth is modulated by other types of limitations, such as translation inhibition or forced expression of useless proteins. Here, we present a single-cell coarse-grained model of bacterial physiology that unifies previous efforts (i.e. the proteome allocation theory and the structural model of division control) into a simple and low-parametric model. We show that this model quantitatively explains the observed relationship between cell size and growth rate for various types of growth limitations with a single free parameter. In addition, predicted proteome fractions agree with observations, and when noise is included in the model, the recently discovered ‘adder’ principle of cell size homeostasis is correctly predicted. Thus, our minimalistic coarse-grained model successfully recapitulates the most fundamental aspects of bacterial physiology, and could serve as a guide for the development of more detailed and mechanistic whole-cell models.
Correlates of end-of-life treatment preferences among young adults and older adults

Abstract The purpose of this study was to investigate correlates of end-of-life treatment preferences. Young adults (n = 117) and older adults (n = 305) completed an interview survey. Compared to older adults, young adults endorsed a desire for more medical intervention in end-of-life scenarios. After controlling for age cohort and education, a desire for more medical intervention in end-of-life scenarios was associated with higher religiosity, greater death anxiety, and more positive attitudes toward aging but not with physical or mental health. End-of-life treatment preferences may be more closely related to attitudes, beliefs, and practices than health status.
Molecular Biology of Mammalian Glucose Transporters.

哺乳動物において、グルコースの摂取とその血漿中の濃度の維持は特異的なトランスポーターによって行われている。 現在、2種類のグルコーストランスポーターの存在が知られている。 Na+との共役によってグルコースを濃度勾配に逆らって能動的に輸送するNa+依存型グルコーストランスポーター (SGLTs)と、促進拡散型グルコーストランスポーター (GLUTs) である。 これらのグルコーストランスポーターは、細胞の分化、癌化及び糖尿病等幾つかの疾病にも関与していると考えられているが、その機構は未だ明らかではない。 分子生物学的手法の導入により、1985年に赤血球型グルコーストランスポーター (GLUT-1) のcDNAがクローニングされて以来、その後の5年間に5種類のGLUTと1種類のSGLTのcDNAがクローニングされた。 これによって、グルコーストランスポーターのアミノ酸配列、細胞膜上での配置及び染色体上の位置など多くの事柄が明らかになった。 今や、グルコーストランスポートの制御機構を分子レベルで研究することが可能になっており、研究は新たな局面を迎えようとしている。
Protective Effect of CXCR4 Antagonist CX807 in a Rat Model of Hemorrhagic Stroke

Intracerebral hemorrhage (ICH) is a major cause of stroke, with high mortality and morbidity. There is no effective pharmacological therapy for ICH. Previous studies have indicated that CXCR4 antagonists reduced microglia activation, attenuated infiltration of T cells, and improved functional recovery in ischemic stroke animals. The interaction of CXCR4 antagonists and ICH has not been characterized. The purpose of this study is to examine the neuroprotective action of a novel CXCR4 antagonist CX807 against ICH. In primary cortical neuronal and BV2 microglia co-culture, CX807 reduced glutamate-mediated neuronal loss and microglia activation. Adult rats were locally administered with collagenase VII to induce ICH. CX807 was given systemically after the ICH. Early post-treatment with CX807 improved locomotor activity in ICH rats. Brain tissues were collected for qRTPCR and histological staining. ICH upregulated the expression of CXCR4, CD8, TNFα, IL6, and TLR4. The immunoreactivity of IBA1 and CD8, as well as TUNEL labeling, were enhanced in the perilesioned area. CX807 significantly mitigated these responses. In conclusion, our data suggest that CX807 is neuroprotective and anti-inflammatory against ICH. CX807 may have clinical implications for the treatment of hemorrhagic stroke.
Molecular taxonomy of the Formica rufa group (red wood ants) (Hymenoptera: Formicidae): a new cryptic species in the Swiss Alps?

Because of their beneficial impact on forest ecosystems, European red wood ants (Formica rufa group) are protected by law in many European countries and are considered to be among the most reliable bioindicators of forest stability. However, their taxonomy has been much debated and, unfortunately, it is too often neglected. This happens mainly because the morphology-based method for species delimitation requires lots of time and experience. We therefore employed 9 microsatellite loci and mitochondrial DNA (COI gene) to verify the power of genetic markers for red wood ant species delimitation and to investigate the cryptic diversity of these ants within the Eastern Swiss Alps. We analyzed 83 nests belonging to all red wood ant species that occur in the Swiss National Park area. Genetic data indicated that these species represent different genetic pools. Moreover, results showed that Formica aquilonia YARROW, 1955 and F. paralugubris SEIFERT, 1996 often hybridize within the Park, confirming that these two species are genetically very close and could have diverged only recently. Nevertheless, microsatellites also revealed that one entire population, located in the Minger Valley and morphologically identified as F. lugubris ZETTERSTEDT, 1838, is genetically different to all other analyzed F. lugubris populations found within the same area and to other red wood ant species. These findings, confirmed by mitochondrial DNA analyses, suggest the existence of a new cryptic species within the Eastern Swiss Alps. This putative cryptic species has been provisionally named F. lugubris-A2. These results have a great importance for future conservation plans, monitoring and evolutionary studies on these protected ants.
Microbial Metabolites, Postbiotics and Intestinal Epithelial Function.

Chronic inflammatory disorders are rising worldwide. The implication of the microbiota in persistent inflammation has been studied for years, but a direct causal relationship has not yet been stablished. Intestinal epithelial cells form a protective barrier against detrimental luminal components. Indeed, a decrease in epithelial integrity may trigger a severe inflammatory reaction due to the infiltration of potentially harmful molecules and microorganisms. Bacterial imbalance, more commonly known as dysbiosis, occurs during inflammation and several strategies have been proposed to counteract this condition. Probiotics have been widely used to positively alter the inherited microbial composition and recover a eubiotic status. Nevertheless, probiotics are thought to impair the return of the indigenous microbiome, and to aggravate inflammation in compromised patients. In contrast, postbiotics - bacterial-free metabolites secreted by probiotic strains - have been proposed as a better and safer. Recent scientific studies that have demonstrated the immunomodulatory properties and epithelial protection of postbiotics are summarized in this review, with an emphasis on the available methods that are currently in use to better understand the role of postbiotics in health and nutrition. This article is protected by copyright. All rights reserved.
Effects of Portland Cement and Polymer Powder on the Properties of Cement-Bound Road Base Mixtures

This article presents the test results for the physical and mechanical properties and fracture toughness of polymer-modified hydraulically-bound mixtures (HBM) produced with Portland cement for road base layers. The modifier used was a redispersible polymer powder (RPP) based on a vinyl ethylene acetate (EVA) copolymer obtained by spray drying. A three-level full factorial design with two factors was applied to determine the contents of Portland cement and polymer powder in the cement-bound mixture (CBM). Both Portland cement and polymer powder were added at three levels: 0%, 2%, and 4%. The assessment included basic physical properties (water absorption, density, and bulk density) and mechanical properties (stiffness modulus, axial compressive strength, and indirect tensile strength) of the CBM. Particular attention was paid to the assessment of fracture toughness in the semi-circular bending test. The results of the research show that polymer powder positively influenced the mechanical properties of CBM by improving its cohesion while maintaining its stiffness. Another benefit coming from the use of polymer powder was the CBM’s increased resistance to cracking, which is the desired characteristic from the perspective of pavement durability.