Miracle-dz/UniFAR-FTUs huggingface dataset:
Linking distortion perception and visual saliency in H.264/AVC coded video containing packet loss

In this paper, distortions caused by packet loss during video transmission are evaluated with respect to their perceived annoyance. In this respect, the impact of visual saliency on the level of annoyance is of particular interest, as regions and objects in a video frame are typically not of equal importance to the viewer. For this purpose, gaze patterns from a task free eye tracking experiment were utilised to identify salient regions in a number of videos. Packet loss was then introduced into the bit stream such as that the corresponding distortions appear either in a salient region or in a non-salient region. A subjective experiment was then conducted in which human observers rated the annoyance of the distortions in the videos. The outcomes show a strong tendency that distortions in a salient region are indeed perceived as much more annoying as compared to distortions in the non-salient region. The saliency of the distorted image content was further found to have a larger impact on the perceived annoyance as compared to the distortion duration. The findings of this work are considered to be of great use to improve prediction performance of video quality metrics in the context of transmission errors.
Dietary Patterns among Asian Indians Living in the United States Have Distinct Metabolomic Profiles That Are Associated with Cardiometabolic Risk.

Background Recent studies, primarily in non-Hispanic whites, suggest that dietary patterns have distinct metabolomic signatures that may influence disease risk. However, evidence in South Asians, a group with unique dietary patterns and a high prevalence of cardiometabolic risk, is lacking. Objective We investigated the metabolomic profiles associated with 2 distinct dietary patterns among a sample of Asian Indians living in the United States. We also examined the cross-sectional associations between metabolomic profiles and cardiometabolic risk markers. Methods We used cross-sectional data from 145 Asian Indians, aged 45-79 y, in the Metabolic Syndrome and Atherosclerosis in South Asians Living in America (MASALA) pilot study. Metabolomic profiles were measured from fasting serum samples. Usual diet was assessed by using a validated food-frequency questionnaire. We used principal components analysis to derive dietary and metabolomic patterns. We used adjusted general linear regression models to examine associations between dietary patterns, individual food groups, metabolite patterns, and cardiometabolic risk markers. Results We observed 2 major principal components or metabolite clusters, the first comprised primarily of medium- to long-chain acylcarnitines (metabolite pattern 1) and the second characterized by branched-chain amino acids, aromatic amino acids, and short-chain acylcarnitines (metabolite pattern 2). A "Western/nonvegetarian" pattern was significantly and positively associated with metabolite pattern 2 (all participants: β ± SE = 0.180 ± 0.090, P = 0.05; participants without type 2 diabetes: β ± SE = 0.323 ± 0.090, P = 0.0005). In all participants, higher scores on metabolite pattern 2 were adversely associated with measures of glycemia (fasting insulin: β ± SE = 2.91 ± 1.29, P = 0.03; 2-h insulin: β ± SE = 22.1 ± 10.3, P = 0.03; homeostasis model assessment of insulin resistance: β ± SE = 0.94 ± 0.42, P = 0.03), total adiponectin (β ± SE = -1.46 ± 0.47, P = 0.002), lipids (total cholesterol: β ± SE = 7.51 ± 3.45, P = 0.03; triglycerides: β ± SE = 14.4 ± 6.67, P = 0.03), and a radiographic measure of hepatic fat (liver-to-spleen attenuation ratio: β ± SE = -0.83 ± 0.42, P = 0.05). Conclusions Our findings suggest that a "Western/nonvegetarian" dietary pattern is associated with a metabolomic profile that is related to an adverse cardiometabolic profile in Asian Indians. Public health efforts to reduce cardiometabolic disease burden in this high-risk group should focus on consuming a healthy plant-based diet.
Erasure Codes for Distributed Storage: Tight Bounds and Matching Constructions

This thesis makes several significant contributions to the theory of both Regenerating (RG) and Locally Recoverable (LR) codes. The two principal contributions are characterizing the optimal rate of an LR code designed to recover from $t$ erased symbols sequentially, for any $t$ and the development of a tight bound on the sub-packetization level (length of a vector code symbol) of a sub-class of RG codes called optimal-access RG codes. There are however, several other notable contributions as well such as deriving the tightest-known bounds on the performance metrics such as minimum distance and rate of a sub-class of LR codes known as availability codes. The thesis also presents some low field size constructions of Maximal Recoverable codes.
Towards functional safety and security for adaptive and flexible business processes

Business process management (BPM) provides many benefits for a company including productivity, efficiency, compliance, risk management, consistency, repeatability, and measurability. Many of these aspects also ensure and improve functional safety, privacy, and security in process execution. However, managed business processes lack flexibility; ie, changing a business process requires more effort than ad hoc execution and adaptation. Thus, especially in small companies, the acceptance rate of managed business processes is low. So we claim that in current BPM approaches, the structuredness ensuring functional safety and security concepts contradicts with the objective for flexibility. The main goal of the AdaBPM project is to address this contradiction by providing a formal approach to handle advanced adaptations and exception handling in business processes. The technical objectives of the project include (1) the definition of a basic framework being capable of handling different levels of adaptivity and considering security and safety requirements at the same time, (2) a rigorous process specification language and model refinement methods, (3) static business process adaptations, and (4) dynamic (or ad hoc) adaptations. The result of our research is a general approach for flexible BPM combined with the possibility to nevertheless manage the process and define safety and security restrictions.
Sound Patch Generation for Vulnerabilities

Security vulnerabilities are among the most critical software defects in existence. As such, they require patches that are correct and quickly deployed. This motivates an automatic patch generation method that emphasizes both soundness and wide applicability. To address this challenge, we propose Senx, which uses three novel patch generation techniques to create patches for out-of-bounds read/write vulnerabilities. Senx uses symbolic execution to extract expressions from the source code of a target application to synthesize patches. To reduce the runtime overhead of patches, it uses loop cloning and access range analysis to analyze loops involved in these vulnerabilities and elevate patches outside of loops. For vulnerabilities that span multiple functions, Senx uses expression translation to translate expressions and place them in a function scope where all values are available to create the patch. This enables Senx to patch vulnerabilities with complex loops and interprocedural dependencies that previous semantics-based patch generation systems cannot handle. We have implemented a prototype using this approach. Our evaluation shows that the patches generated by Senx successfully fix 76% of 42 real-world vulnerabilities from 11 applications including various tools or libraries for manipulating graphics/media files, a programming language interpreter, a relational database engine, a collection of programming tools for creating and managing binary programs, and a collection of basic file, shell, and text manipulation tools. All patches that Senx produces are sound, and Senx correctly aborts patch generations in cases where its analysis will fall short.
Dedifferentiated adenoid cystic carcinoma ex pleomorphic adenoma of the parotid

Carcinoma ex pleomorphic adenoma (Ca ex PA) is defined as a carcinoma arising from a primary (de novo) or recurrent benign pleomorphic adenoma. The most common histological subtype is adenocarcinoma, not otherwise specified, salivary duct carcinoma, mucoepidermoid carcinoma, and adenoid cystic carcinoma (ACC). Few case reports of de novo dedifferentiation in ACC are there in the literature, mostly involving minor salivary glands. The dedifferentiated adenoid cystic carcinoma arising in a pleomorphic adenoma of the parotid gland has not been reported earlier. The present case highlights this rare histological subtype seen in Ca ex PA and the role of extensive histopathological examination and immunohistochemistry.
Prevalence and progression of chronic kidney disease after liver transplant: a prospective, real-life, observational, two-year multicenter study.

INTRODUCTION chronic kidney disease is a frequent complication after liver transplantation. The use of calcineurin inhibitors is one of the causes of this complication. Current immunsuppression regimens that reduce the use of calcineurin inhibitors may be associated with an improved preservation of renal function. OBJECTIVE the study aimed to assess the evolution of renal function after liver transplantation in the current routine clinical practice. METHODS an observational, prospective, multicenter study in adult liver transplant recipients was performed. Two hundred and thirty patients with a good renal function before transplantation were assessed six months post-transplantation (baseline) and every six months until month 30. RESULTS at baseline, 32% of the patients had a reduction in the glomerular filtration rate below < 60 ml/min/1.73 m2. The mean glomerular filtration rate increased from 72.3 to 75.6 ml/min/1.73 m2 at baseline and month 30 respectively (p < 0.01). The mean serum creatinine levels (mg/dl) decreased from 1.13 to 1.09 (p < 0.01). The percentage of patients with stage 3 chronic kidney disease decreased from 31.7% to 26.4%, whereas the percentage of patients with stage 4 remained unchanged (0.4% at baseline and 0.5% at month 30). No patients progressed to end-stage kidney disease that required dialysis or renal transplantation. CONCLUSION in the routine clinical practice, a moderate deterioration of renal function is frequent after liver transplantation. However, advanced chronic kidney disease is infrequent in patients with a good pre-transplant renal function.
Chemoproteomics reveals baicalin activates hepatic CPT1 to ameliorate diet-induced obesity and hepatic steatosis

Significance Baicalin is a major flavonoid component from the herbal medicine Scutellaria baicalensis that has been shown to have an antisteatosis effect. Through quantitative chemoproteomic profiling, we discovered that baicalin acts as a natural allosteric activator of carnitine palmitoyltransferase 1 (CPT1), the rate-limiting enzyme of fatty acid β-oxidation (FAO). By directly binding to CPT1 and activating its activity to accelerate fatty acid degradation, baicalin can significantly ameliorate symptoms associated with hepatic steatosis and reduce diet-induced obesity (DIO). Our study provides an example of a natural product agonist for CPT1. The results provide mechanistic insights to explain the bioactivity of baicalin in reducing lipid accumulation and introduce exciting opportunities for developing novel flavonoid-based FAO activators for pharmacologically treating DIO and associated metabolic disorders. Obesity and related metabolic diseases are becoming worldwide epidemics that lead to increased death rates and heavy health care costs. Effective treatment options have not been found yet. Here, based on the observation that baicalin, a flavonoid from the herbal medicine Scutellaria baicalensis, has unique antisteatosis activity, we performed quantitative chemoproteomic profiling and identified carnitine palmitoyltransferase 1 (CPT1), the controlling enzyme for fatty acid oxidation, as the key target of baicalin. The flavonoid directly activated hepatic CPT1 with isoform selectivity to accelerate the lipid influx into mitochondria for oxidation. Chronic treatment of baicalin ameliorated diet-induced obesity (DIO) and hepatic steatosis and led to systemic improvement of other metabolic disorders. Disruption of the predicted binding site of baicalin on CPT1 completely abolished the beneficial effect of the flavonoid. Our discovery of baicalin as an allosteric CPT1 activator opens new opportunities for pharmacological treatment of DIO and associated sequelae.
EviNet: a web platform for network enrichment analysis with flexible definition of gene sets

Abstract The new web resource EviNet provides an easily run interface to network enrichment analysis for exploration of novel, experimentally defined gene sets. The major advantages of this analysis are (i) applicability to any genes found in the global network rather than only to those with pathway/ontology term annotations, (ii) ability to connect genes via different molecular mechanisms rather than within one high-throughput platform, and (iii) statistical power sufficient to detect enrichment of very small sets, down to individual genes. The users’ gene sets are either defined prior to upload or derived interactively from an uploaded file by differential expression criteria. The pathways and networks used in the analysis can be chosen from the collection menu. The calculation is typically done within seconds or minutes and the stable URL is provided immediately. The results are presented in both visual (network graphs) and tabular formats using jQuery libraries. Uploaded data and analysis results are kept in separated project directories not accessible by other users. EviNet is available at https://www.evinet. org/.
Comparing Digital Phase-Locked Loop and Kalman Filter for Clock Tracking in Ultrawideband Location System

For timing and synchronization system, digital phase-locked loop (DPLL) and Kalman filter all have been widely used as the clock tracking and clock correction schemes for the similar structure and properties. This paper compares the two schemes used for ultrawideband (UWB) location system. The improved Kalman filter is more immune to interference.
MAP spatial pyramid mean shift for object tracking

Mean Shift is popular in object tracking due to its simplicity and efficiency. It finds local maximum of the similarity measure between the target model and target candidate, and works well in many situations. However, it suffers from two aspects. First, Mean Shift tracker ignores background knowledge. As a result, it may fail when the background color is similar to that of the target or the initial target region contains too much background. Second, Mean Shift tracker omits the geometric structure with a global color histogram as the target model. Therefore, it may not work in the case of partial occlusion. To solve the first problem, we introduce background color histogram into a MAP formulation. To address the second problem, we divide the target into hierarchical blocks. These blocks are described with a histogram each but tracked as a whole. The two threads lead to a new algorithm, named MAP spatial pyramid (MAP-SP) Mean Shift. The efficiency of MAP-SP Mean Shift is demonstrated via comparative experiments on both standard and our own video sequences
“Disruptor” residues in the regulator of G protein signaling (RGS) R12 subfamily attenuate the inactivation of Gα subunits

Specific amino acids within RGS proteins may encode specificity toward G protein α subunits. Designing specificity Once an agonist binds to its G protein–coupled receptor, GTP replaces GDP on the α subunit of an associated G protein, which then dissociates from its βγ dimer to activate effectors. The GTPase activity of the α subunit returns the G protein to an inactive state, a process that is accelerated by interactions with members of the regulator of G protein signaling (RGS) family. Asli et al. used functional and structural analyses to identify specific amino acid residues that distinguished RGS proteins with low activity toward Gαo from those with high activity. High-activity RGS proteins that were mutated to contain these “disruptor” residues exhibited reduced inhibitory activity toward the Gα subunit. Together, these data suggest that “disruptor” residues within RGS proteins may encode specificity toward Gα subunits. Understanding the molecular basis of interaction specificity between RGS (regulator of G protein signaling) proteins and heterotrimeric (αβγ) G proteins would enable the manipulation of RGS-G protein interactions, explore their functions, and effectively target them therapeutically. RGS proteins are classified into four subfamilies (R4, R7, RZ, and R12) and function as negative regulators of G protein signaling by inactivating Gα subunits. We found that the R12 subfamily members RGS10 and RGS14 had lower activity than most R4 subfamily members toward the Gi subfamily member Gαo. Using structure-based energy calculations with multiple Gα-RGS complexes, we identified R12-specific residues in positions that are predicted to determine the divergent activity of this subfamily. This analysis predicted that these residues, which we call “disruptor residues,” interact with the Gα helical domain. We engineered the R12 disruptor residues into the RGS domains of the high-activity R4 subfamily and found that these altered proteins exhibited reduced activity toward Gαo. Reciprocally, replacing the putative disruptor residues in RGS18 (a member of the R4 subfamily that exhibited low activity toward Gαo) with the corresponding residues from a high-activity R4 subfamily RGS protein increased its activity toward Gαo. Furthermore, the high activity of the R4 subfamily toward Gαo was independent of the residues in the homologous positions to the R12 subfamily and RGS18 disruptor residues. Thus, our results suggest that the identified RGS disruptor residues function as negative design elements that attenuate RGS activity for specific Gα proteins.
Dank Learning: Generating Memes Using Deep Neural Networks

We introduce a novel meme generation system, which given any image can produce a humorous and relevant caption. Furthermore, the system can be conditioned on not only an image but also a user-defined label relating to the meme template, giving a handle to the user on meme content. The system uses a pretrained Inception-v3 network to return an image embedding which is passed to an attention-based deep-layer LSTM model producing the caption - inspired by the widely recognised Show and Tell Model. We implement a modified beam search to encourage diversity in the captions. We evaluate the quality of our model using perplexity and human assessment on both the quality of memes generated and whether they can be differentiated from real ones. Our model produces original memes that cannot on the whole be differentiated from real ones.
Query expansion based on statistical learning from code changes

Thesaurus‐based, code‐related, and software‐specific query expansion techniques are the main contributions in free‐form query search. However, these techniques still could not put the most relevant query result in the first position because they lack the ability to infer the expansion words that represent the user needs based on a given query. In this paper, we discover that code changes can imply what users want and propose a novel query expansion technique with code changes (QECC). It exploits (changes, contexts) pairs from changed methods. On the basis of statistical learning from pairs, it can infer code changes for a given query. In this way, it expands a query with code changes and recommends the query results that meet actual needs perfectly. In addition, we implement InstaRec to perform QECC and evaluate it with 195 039 change commits from GitHub and our code tracker. The results show that QECC can improve the precision of 3 code search algorithms (ie, IR, Portfolio, and VF) by up to 52% to 62% and outperform the state‐of‐the‐art query expansion techniques (ie, query expansion based on crowd knowledge and CodeHow) by 13% to 16% when the top 1 result is inspected.
Existence of NEU1 sialidase on mouse thymocytes whose natural substrate is CD5

Membrane-bound sialidases in the mouse thymus are unique and mysterious because their activity at pH 6.5 is equal to or higher than that in the acidic region. The pH curve like this has never been reported in membrane-bound form. To clarify this enzyme, we studied the sialidase activities of crude membrane fractions from immature-T, mature-T and non-T cells from C57BL/6 mice and from SM/J mice, a strain with a defect in NEU1 activity. Non-T cells from C57BL/6 mice had high activity at pH 6.5, but those from SM/J mice did not. Neu1 and Neu3 mRNA was shown by real-time PCR to be expressed in T cells and also in non-T cells, whereas Neu2 was expressed mainly in non-T cells and Neu4 was scarcely expressed. However, the in situ hybridization study on the localization of four sialidases in the thymus showed that Neu4 was clearly expressed. We then focused on a sialidase on the thymocyte surface because the possibility of the existence of a sialidase on thymocytes was suggested by peanut agglutinin (PNA) staining after incubation of the cells alone in PBS. This activity was inhibited by NEU1-selective sialidase inhibitor C9-butyl-amide-2-deoxy-2,3-dehydro-N-acetylneuraminic acid. The natural substrate for the cell surface sialidase was identified as clustered differentiation 5 (CD5) by PNA-blot analysis of anti-CD5 immunoprecipitate. We conclude that NEU1 exists on the cell surface of mouse thymocytes and CD5 is a natural substrate for it. Although this is not the main reaction of the membrane-bound thymus-sialidases, it must be important for the thymus.
Changes in dominant Escherichia coli and antimicrobial resistance after 24 hr in fecal matter

Intestinal bacteria carry antimicrobial resistance (AMR) genes in mobile genetic elements which have the potential to spread to bacteria in other animal hosts including humans. In fecal matter, Escherichia coli can continue to multiply for 48 hr after being excreted, and in certain environments, E. coli survive long periods of time. It is unclear the extent to which AMR in E. coli changes in the environment outside of its host. In this study, we analyzed changes in the population structure, plasmid content, and AMR patterns of 30 E. coli isolates isolated from 6 chickens (cloacal swabs), and 30 E. coli isolates from fecal samples (from the same 6 chickens) after 24 hr of incubation. Clonality of isolates was screened using the fumC gene sequence and confirmed in a subset of isolates (n = 14) by multi‐locus sequence typing. Major shifts in the population structure (i.e., sequence types) and antibiotic resistance patterns were observed among the numerically dominant E. coli isolates after 24 hr. Four E. coli clones isolated from the cloaca swabs and the corresponding fecal samples (after 24 hr incubation) showed different antibiotic resistance patterns. Our study reveals that fecal matter in the environment is an intermediate habitat where rapid and striking changes occur in E. coli populations and antibiotic resistance patterns.