Miracle-dz/UniFAR-FTUs huggingface dataset:
Colored Network Motif Analysis by Dynamic Programming Approach: An Application in Host Pathogen Interaction Network

Network motifs are subgraphs of a network which are found with significantly higher frequency than that expected in similar random networks. Motifs are small building blocks of a network and they have emerged as a way to uncover topological properties of complex networks. A special yet not much explored type of motif is the ‘colored motif’ where color (type) of each node, and hence the edges, in the motif is distinguishable from each other. A traditional motif is defined as a recurring structure in a network, whereas colored motif introduces detailed information about the color of the nodes. G-trie is a data structure to efficiently store a given set of subgraphs by exploiting the topological overlaps within them. In this article we have implemented a modified g-trie to store colored subgraphs and developed a method to discover colored motifs. Our method uses an approximate enumeration for counting the subgraphs to reduce the runtime. We have applied our method to find colored motifs of size three in a host pathogen protein-protein interaction network having two types of proteins namely HIV-1 and human proteins, and four types of edges. Here, we have discovered eight motifs, six of which contain both HIV-1 and human proteins, while the remaining two contain only human proteins.
Focusing and Description in Natural Language Dialogues

Abstract : When two people talk, they focus their attention on only a small portion of what each of them knows or believes. Both what is said and how it is interpreted depend on a shared understanding of this narrowing of attention to a small highlighted portion of what is known. Focusing is an active process. As a dialogue progresses, the participants continually shift their focus and thus form an evolving context against which utterances are produced and understood. A speaker provides a hearer with clues of what to look at and how to look at it what to focus on, how to focus on it, and how wide or narrow the focusing should be. As a result, one of the effects of understanding an utterance is that the listener becomes focused on certain entities (both objects and relationships) from a particular perspective. Focusing clues may be linguistic or they may come from knowledge about the relationships between entities in the domain. Linguistic clues may be either explicit, deriving directly from certain words, or implicit, deriving from sentential structure and from rhetorical relationships between sentences. This paper examines the relationship between focusing and definite descriptions in dialogue and its implications for natural language processing systems. It describes focusing mechanisms based on domain- structure clues which have been included in a computer system and, from this perspective, indicates future research problems entailed in modeling the focusing process more generally.
Randomized phase II trial of survivin 2B peptide vaccination for patients with HLA‐A24‐positive pancreatic adenocarcinoma

The prognosis of advanced pancreatic adenocarcinoma is still extremely poor. This study sought to determine the efficacy of, and immunological response to, peptide vaccination therapy in patients with this disease. In this multicenter randomized phase II study, patients with advanced pancreatic adenocarcinoma after gemcitabine and/or tegafur/gimeracil/oteracil were randomly assigned to 3 groups that each received a 2‐step treatment course. In Step 1, the groups received treatments of: (i) survivin 2B peptide (SVN‐2B) plus interferon‐β (IFNβ); (ii) SVN‐2B only; or (iii) placebo until the patients show progression. In Step 2, all patients who consented to participate received 4 treatments with SVN‐2B plus IFNβ. The primary endpoint was progression‐free survival (PFS) after initiation of Step 1 treatment. Secondary endpoints included immunological effects assessed by analysis of PBMCs after Step 1. Eighty‐three patients were randomly assigned to receive SVN‐2B plus IFNβ (n = 30), SVN‐2B (n = 34), or placebo (n = 19). No significant improvement in PFS was observed. Survivin 2B‐specific CTLs were found to be increased in the SVN‐2B plus IFNβ group by tetramer assay. Among patients who participated in Step 2, those who had received SVN‐2B plus IFNβ in Step 1 showed better overall survival compared with those who had received placebo in Step 1. Patients vaccinated with SVN‐2B plus IFNβ did not have improved PFS, but showed significant immunological reaction after vaccination. Subgroup analysis suggested that a longer SVN‐2B plus IFNβ vaccination protocol might confer survival benefit. (Clinical trial registration number: UMIN 000012146).
Vasopressin Cells in the Rodent Olfactory Bulb Resemble Non-Bursting Superficial Tufted Cells and Are Primarily Inhibited upon Olfactory Nerve Stimulation

Abstract The intrinsic vasopressin system of the olfactory bulb is involved in social odor processing and consists of glutamatergic vasopressin cells (VPCs) located at the medial border of the glomerular layer. To characterize VPCs in detail, we combined various electrophysiological, neuroanatomical, and two-photon Ca2+ imaging techniques in acute bulb slices from juvenile transgenic rats with eGFP-labeled VPCs. VPCs showed regular non-bursting firing patterns, and displayed slower membrane time constants and higher input resistances versus other glutamatergic tufted cell types. VPC axons spread deeply into the external plexiform and superficial granule cell layer (GCL). Axonal projections fell into two subclasses, with either denser local columnar collaterals or longer-ranging single projections running laterally within the internal plexiform layer and deeper within the granule cell layer. VPCs always featured lateral dendrites and a tortuous apical dendrite that innervated a single glomerulus with a homogenously branching tuft. These tufts lacked Ca2+ transients in response to single somatically-evoked action potentials and showed a moderate Ca2+ increase upon prolonged action potential trains. Notably, electrical olfactory nerve stimulation did not result in synaptic excitation of VPCs, but triggered substantial GABAA receptor-mediated IPSPs that masked excitatory barrages with yet longer latency. Exogenous vasopressin application reduced those IPSPs, as well as olfactory nerve-evoked EPSPs recorded from external tufted cells. In summary, VPCs can be classified as non-bursting, vertical superficial tufted cells. Moreover, our findings imply that sensory input alone cannot trigger excitation of VPCs, arguing for specific additional pathways for excitation or disinhibition in social contexts.
The role of advance preparation in simultaneous interpreting: A comparison of professional interpreters and interpreting students

Current comprehension models recognize the role of prior topic-specific knowledge in the processing of general and specialized discourse (e.g. Gernsbacher 1990; Johnson-Laird 1983; Kintsch 1988). In interpreting, there is widespread consensus that interpreters work better when they prepare in advance. However, research on how preparation affects interpreting has encountered such methodological challenges as high variability and the need for appropriately sensitive measures and tasks (Gile 2005). This article reports an experimental study to assess the effect of advance preparation on simultaneous interpreting of specialized speeches, comparing seven professional interpreters and sixteen interpreting students. All participants did two simultaneous interpretations, into Spanish (their ‘A’ language) from English, of presentations from scientific congresses: one with preparation materials provided half an hour beforehand, the other without preparation. Each source text contained both ‘neutral’ and ‘difficult’ speech segments (the three types of difficulty being terminology, syntactic complexity and lack of redundancy). Dependent variables were accuracy of interpretation and length of ear-voice span (EVS), the rationale being that longer EVS probably reflects processing difficulties. The results show that both groups worked significantly better after advance preparation, this being reflected both in accuracy and in ability to maintain a shorter EVS. Interaction between preparation and type of difficulty was also examined.
Measurements and Models of One-Way Transit Time in IP Routers

The main goals of this thesis are towards an understanding of the delay process in best-effort Internet for both non-congested and congested networks. A novel measurement system is reported for delay measurements in IP routers, which follows specifications of the IETF RFC 2679. The system employs both passive measurements and active probing and offers the possibility to measure and analyze different delay components of a router, e.g., packet processing delay, packet transmission time and queueing delay at the output link. Dedicated application-layer software is used to generate UDP traffic with TCP-like characteristics. Pareto traffic models are used to generate self-similar traffic in the link. The reported results are in form of several important statistics regarding processing and queueing delays of a router, router delay for a single data flow, router delay for multiple data flows as well as end-to-end delay for a chain of routers. They confirm results reported earlier about the fact that the delay in IP routers is generally influenced by traffic characteristics, link conditions and, to some extent, details in hardware implementation and different IOS releases. The delay in IP routers may also occasionally show extreme values, which are due to improper functioning of the routers. Furthermore, new results have been obtained that indicate that the delay in IP routers shows heavy-tailed characteristics, which can be well modeled with the help of several distributions, either in the form of a single distribution or as a mixture of distributions. There are several components contributing to the OWTT in routers, i.e., processing delay, queueing delay and service time. The obtained results have shown that, e.g., the processing delay in a router can be well modeled with the Normal distribution, and the queueing delay is well modeled with a mixture of Normal distribution for the body probability mass and Weibull distribution for the tail probability mass. Furthermore, OWTT has several component delays and it has been observed that the component delay distribution that is most dominant and heavy-tailed has a decisive influence on OWTT.
Production of nonnatural straight-chain amino acid 6-aminocaproate via an artificial iterative carbon-chain-extension cycle

Bioplastics produced from microbial source are promising green alternatives to traditional petrochemical-derived plastics. Nonnatural straight-chain amino acids, especially 5-aminovalerate, 6-aminocaproate and 7-aminoheptanoate are potential monomers for the synthesis of polymeric bioplastics as their primary amine and carboxylic acid are ideal functional groups for polymerization. Previous pathways for 5-aminovalerate and 6-aminocaproate biosynthesis in microorganisms are derived from L-lysine catabolism and citric acid cycle, respectively. Here, we show the construction of an artificial iterative carbon-chain-extension cycle in Escherichia coli for simultaneous production of a series of nonnatural amino acids with varying chain length. Overexpression of L-lysine α-oxidase in E. coli yields 2-keto-6-aminocaproate as a non-native substrate for the artificial iterative carbon-chain-extension cycle. The chain-extended α-ketoacid is subsequently decarboxylated and oxidized by an α-ketoacid decarboxylase and an aldehyde dehydrogenase, respectively, to yield the nonnatural straight-chain amino acid products. The engineered system demonstrated simultaneous in vitro production of 99.16 mg/L of 5-aminovalerate, 46.96 mg/L of 6-aminocaproate and 4.78 mg/L of 7-aminoheptanoate after 8 hours of enzyme catalysis starting from 2-keto-6-aminocaproate as the substrate. Furthermore, simultaneous production of 2.15 g/L of 5-aminovalerate, 24.12 mg/L of 6-aminocaproate and 4.74 mg/L of 7-aminoheptanoate was achieved in engineered E. coli. This work illustrates a promising metabolic-engineering strategy to access other medium-chain organic acids with -NH2,-SCH3, -SOCH3, -SH, -COOH, -COH, or -OH functional groups through carbon-chain-elongation chemistry.
Effect of Temperature and Tissue Type on the Development of the Forensic Fly Chrysomya megacephala (Diptera: Calliphoridae)

Abstract Chrysomya megacephala Fabricius is one of the most common myiasis-causing and carrion-feeding fly species in the tropics. This species has a worldwide distribution due to globalization and therefore is of critical importance to the public health sector and forensic investigations. Development studies carried worldwide show that Ch. megacephala reared at similar temperatures may require different amounts of time to complete their cycle of growth. The present study determined for the first time the life-history information of this species in Sri Lanka. Chrysomya megacephala colonies were reared on three different food sources (bovine muscle, swine muscle, and swine liver) considering the most common forensic entomology rearing mediums and the capability of Ch. megacephala to cause myiasis in cattle. Furthermore, colonies were reared at four temperature regimes representing several specific development conditions of this blowfly: 1) 20°C representing the estimation of the lower developmental threshold for this species in Sri Lanka; 2) 25 and 27°C representing typical room/environmental temperatures in Sri Lanka; and 3) 38°C as this is the typical living animal temperature, representing myiasis conditions. Results show that temperature significantly affected larval length and width over time; however, tissue type was not a significant factor. The fastest development was recorded at 38°C for immature feeding on bovine muscle (162.15 h), followed by those fed swine liver (184.15 h) and swine muscle (208.00 h). The calculated minimum temperature threshold for Ch. megacephala was 13°C. Data generated will be crucial for future forensic investigations involving living or deceased individuals colonized by this species.
Organizational culture and socio-cultural values: perceptions of managers and employees in five economies in transition

This survey-based study compared socio-cultural values and perceptions of organizational culture characteristics held by more than 3,300 managers and employees in twelve business organizations in Hungary, Russia, Georgia, Kazakhstan, and the Kyrgyz Republic. Significant differences were found between the five countries on all socio-cultural and organizational culture dimensions. The relationship between socio-cultural values and the organizational culture perceptions was only moderately significant. The paper concludes with implications for professionals seeking to enhance organizations' performance in these countries and suggestions for further research.
Cardiopulmonary Function in Patients with Congenital Scoliosis: An Observational Study.

BACKGROUND Patients with congenital scoliosis often have restrictive pulmonary dysfunction on static pulmonary function testing (PFT). Although frequently asymptomatic during daily activities, these patients are generally assumed to have reduced exercise capacity. The aim of this study was to use dynamic cardiopulmonary exercise testing (CPET) to investigate exercise capacity and its association with spinal deformity in patients with congenital scoliosis. METHODS Sixty patients with congenital scoliosis who underwent preoperative spinal radiography, PFT, and CPET were included from January 2014 to November 2017. The impact of thoracic spinal deformity and rib anomalies on pulmonary function and physical capacity was investigated. RESULTS A significant deterioration in pulmonary function with increases in the severity of the major thoracic curve was demonstrated by the forced expiratory volume in 1 second (FEV1), forced vital capacity (FVC), and total lung capacity (all p < 0.001). The ratio of FEV1 to FVC was similar regardless of thoracic curve severity. A smaller tidal volume during exercise testing reflected restrictive dysfunction in the patients with the most severe curves. CPET also revealed a significant trend of faster breathing by patients with a severe thoracic curve (p < 0.001). Exercise capacity indicators such as work rate (p = 0.019), heart rate (p = 0.015), and oxygen saturation (p = 0.006) were significantly reduced only in patients with a thoracic curve of >100°. Pulmonary dysfunction was the major contributor to exercise intolerance. Compared with mild pulmonary dysfunction, moderate and severe dysfunction was associated with an abnormal breathing pattern and lower work rate (p = 0.032) and peak oxygen intake (p = 0.042), indicating worse exercise tolerance. CONCLUSIONS Congenital scoliosis leads to restrictive pulmonary dysfunction, which reduces the tidal volume and forces patients to accelerate respiratory rates during exercise. Patients with a thoracic curve of >100° are unable to compensate and have significantly reduced exercise capacity. LEVEL OF EVIDENCE Prognostic Level II. See Instructions for Authors for a complete description of levels of evidence.
A Brief History of an Ethnographic Database

Abstract Since 1950, the Human Relations Area Files, Inc. has produced what is currently known as the eHRAF Collection of Ethnography. This article explores the reasons why it was created and describes the structure of this complex collection of ethnographic works. Over time, this resource has been produced in four different formats: paper slips, microfiche, CD-ROM, and online. The similarities among and differences between these are discussed. An attempt to locate any remaining paper sets is described, and a list of current locations of the file in this, its original form, is included.
Somite development in the avian tail

Somites are epithelial segments of the paraxial mesoderm. Shortly after their formation, the epithelial somites undergo extensive cellular rearrangements and form specific somite compartments, including the sclerotome and the myotome, which give rise to the axial skeleton and to striated musculature, respectively. The dynamics of somite development varies along the body axis, but most research has focused on somite development at thoracolumbar levels. The development of tail somites has not yet been thoroughly characterized, even though vertebrate tail development has been intensely studied recently with respect to the termination of segmentation and the limitation of body length in evolution. Here, we provide a detailed description of the somites in the avian tail from the beginning of tail formation at HH‐stage 20 to the onset of degeneration of tail segments at HH‐stage 27. We characterize the formation of somite compartment formation in the tail region with respect to morphology and the expression patterns of the sclerotomal marker gene paired‐box gene 1 (Pax1) and the myotomal marker genes MyoD and myogenic factor 5 (Myf5). Our study gives insight into the development of the very last segments formed in the avian embryo, and provides a basis for further research on the development of tail somite derivatives such as tail vertebrae, pygostyle and tail musculature.
ETIOSARC study : environmental aetiology of sarcomas from a French prospective multicentric population-based case–control study—study protocol

Introduction Sarcomas are rare tumours of connective tissue. The exact overall incidence of sarcomas is unknown due to diagnostic difficulties and the various histological subtypes (over 80 subtypes). However, the apparent increasing incidence of sarcomas suggests environmental causes such as pesticides. Except for some specific factors (ie, ionising radiation, vinyl chloride, dioxin and genetic predispositions) the scientific knowledge on the aetiology of sarcomas is sparse and inconsistent. France is a particularly appropriate country to set up a study investigating the causes of sarcoma occurrence due to the French organisation in treatment and care of sarcoma patients, which is highly structured and revolved around national expert networks. The main objective of the ETIOlogy of SARcomas (ETIOSARC) project is to study the role of lifestyle, environmental and occupational factors in the occurrence of sarcomas among adults from a multicentric population-based case–control study. Methods and analysis Cases will be all incident patients (older than 18 years) prospectively identified in 15 districts of France covered by a general population-based cancer registry and/or a reference centre in sarcoma’s patient care over a 3-year period with an inclusion start date ranging from February 2019 to January 2020 and histologically confirmed by a second review of the diagnosis. Two controls will be individually matched by sex, age (5 years group) and districts of residence and randomly selected from electoral rolls. A standardised questionnaire will be administered by a trained interviewer in order to gather information about occupational and residential history, demographic and socioeconomic characteristics and lifestyle factors. At the end of the interview, a saliva sample will be systematically proposed. This study will permit to validate or identify already suspected risk factors for sarcomas such as phenoxyherbicides, chlorophenol and to generate new hypothesis to increase our understanding about the genetic and environmental contributions in the carcinogenicity process. Ethics and dissemination The present study is promoted by the French National Institute of Health and Medical Research (identification number C17-03). This study received National French Ethic committee (CPP Sud Méditerrannée I) approval (identification number 18-31) and French Data Protection Authority (CNIL) approval (identification number 918171). Results of this study will be published in international peer-reviewed journals. Technical appendix, statistical code and dataset will be available in the Dryad repository when collection data are completed. Trial registration number NCT03670927.
Single image super-resolution using sparse prior

Obtaining high-resolution images from low-resolution ones has been an important topic in computer vision field. This is a very hard problem since low-resolution images will always lose some information when down sampled from high-resolution ones. In this article, we proposed a novel image super-resolution method based on the sparse assumption. Compared to many existing example-based image super-resolution methods, our method is based on single original low-resolution image, i.e. our method does not need any training examples. Compared to other interpolation based approach, like nearest neighbor, bilinear or bicubic, our method takes advantage of the inner properties of high-resolution images, thus obtains a better result. The main approach for our method is based on the recently developed theory called sparse representation and compress sensing. Many experiments show our method can lead to competitive or even superior results in quality to images produced by other super-resolution methods, while our method need much fewer additional information.