Miracle-dz/UniFAR-FTUs huggingface dataset:
Monoclonality or oligoclonality of human herpesvirus 8 terminal repeat sequences in Kaposi's sarcoma and other diseases.

BACKGROUND Infection with human herpesvirus 8 (HHV8), also termed Kaposi's sarcoma (KS)-associated herpesvirus, is associated with all forms of KS, with primary effusion lymphoma (PEL), and with some forms of multicentric Castleman's disease (MCD), but the pathogenic role of HHV8 in these tumors and the clonal nature of KS are still unclear. The purpose of this study was to examine whether the number of terminal repeats (TRs) contained in the fused TR region of HHV8 could be used as a marker of clonality in HHV8-associated tumors. METHODS Pulsed-field gel electrophoresis (PFGE) and multiple-probe Southern blot analysis of the HHV8 TR region were performed on high-molecular-weight DNA obtained from tumoral KS, PEL, and MCD lesions. RESULTS These analysis showed that the fused TR region contains a large but variable number of TR units (ranging from 16 to 75) and that the viral genome is present as extrachromosomal circular DNA in these tumors in vivo, with occasional ladders of heterogeneous linear termini reflecting lytic replication. All PEL tumors and PEL-derived cell lines as well as some KS tumors contained monoclonal or oligoclonal fused TR fragments; however, the TR region appeared polyclonal in MCD tumors and in a few KS lesions. CONCLUSION Several KS and PEL lesions are monoclonal expansions of a single infected cell, suggesting that HHV8 infection precedes tumor growth and thus supporting an etiologic role of latent HHV8 in these proliferations. Our finding that nodular KS lesions display all possible patterns of clonality supports the model according to which KS begins as a polyclonal disease with subsequent evolution to a monoclonal process.
MicroRNA-200a inhibits epithelial-mesenchymal transition in human hepatocellular carcinoma cell line.

OBJECTIVE Our study investigated the role of microRNA (miR)-200a and its molecular targets in hepatocellular carcinoma (HCC) cells. METHODS An inhibitor of miR-200a was transiently transfected into the hepatocellular carcinoma cell line, MHCC-97L. The effect of this transfection on mRNA levels of epithelial-mesenchymal transition (EMT)-related genes was measured by fluorescence-based quantitative real-time polymerase chain reaction (qRT-PCR). Further, protein levels of EMT-related genes, cell proliferation and apoptosis-related markers were assessed by Western blot analysis in these transfected cells. MTT and wound-healing assay were used to evaluate the proliferation and migration of MHCC-97L cells in presence and in absence of miR-200a inhibitor. RESULTS Compared with miR-NC control group, qRT-PCR results in anti-miR-200a group revealed a significant reduction in the mRNA levels of E-cadherin, with a concomitant increasing in vimentin mRNA level (all P < 0.05). Western blot results showed higher E-cadherin and Caspase-3 protein expressions in anti-miR-200a group compared to miR-NC group (P < 0.05). In addition, vimentin and Ki-67 protein expression was found sharply decreased in anti-miR-200a group compared to miR-NC group (P < 0.05). Consistent with this, wound-healing and MTT assay showed that migration and proliferation capacity of MHCC-97L cells in anti-miR-200a group is significantly increased compared with miR-NC group (both P < 0.05). CONCLUSION Our study reveals an important role of miR-200a in inhibiting EMT, proliferation and migration in HCC cells, suggesting the possibility of miR-200a-based therapeutics in HCC.
1 New techniques for detection and adjustment of shifts in daily precipitation data series

This study integrates a Box-Cox power transformation procedure into a common trend two-phase regression model based test (the PMFred algorithm) for detecting changepoints, to make the test applicable to non-Gaussian data series, such as non-zero daily precipitation amounts or wind speeds. The detection power aspects of the transformed method (transPMFred) are assessed by a simulation study, which shows that this new algorithm is much better than the corresponding untransformed method for non-Gaussian data; the transformation procedure can increase the hit rate by up to about 70%. Examples of application of this new transPMFred algorithm to detect shifts in real daily precipitation series are provided using non-zero daily precipitation series recorded at a few stations across Canada that represent very different precipitation regimes. The detected changepoints are in good agreement with documented times of changes in for all the example series. This study clarifies that it is essential for homogenization of daily precipitation data series to test the non-zero precipitation amount series and the frequency series of precipitation occurrence (or non-occurrence), separately. The new transPMFred can be used to test the series of non-zero daily precipitation (which are non-Gaussian and positive), while the existing PMFred algorithm can be used to test the frequency series. A software package for using the transPMFred algorithm to detect shifts in non-zero daily precipitation amounts has been developed and made available online free of charge, along with a quantile matching (QM) algorithm for adjusting shifts in non-zero daily precipitation series, which is applicable to all positive data. In addition, a similar QM algorithm has also been developed for adjusting Gaussian data such as temperatures. It is noticed that frequency discontinuities are often inevitable due to changes in the measuring precision of precipitation, and that they could complicate the detection of shifts in non-zero daily precipitation data series and void any attempt to homogenize the
Morphine-induced stereotyped thigmotaxis could appear as enhanced fear and anxiety in some behavioural tests

This study questions whether the classical interpretation for unconditional fear/anxiety tests is valid when animals are under the influence of some drugs of abuse. We used a modified version of the trimethylthiazoline (TMT)—avoidance task, a measure of unconditional fear. Halfway into a corridor maze we placed a 3-cm-high barrier. This provided a wall in the middle of the corridor, one that the mice can easily climb over. Saline- and morphine-treated mice were randomly placed in the ‘safe’ or ‘unsafe’ (TMT) side and observed for 10 min. As expected, saline-injected mice spent only about 25% of the time in the TMT side, regardless of the side they were initially placed into. In contrast, morphine-treated mice did not cross the barrier even once, regardless of their initial placement. Specifically, morphine-treated mice initially placed in the TMT side appeared to exhibit the expected reduction in unconditional fear, that is, spending the entire time in the TMT side, a significant increase over the controls. Yet, morphine-treated mice placed in the safe side never even entered the TMT side; thus, these mice appeared to exhibit a behavioural response that is classically interpreted as increased fear, that is, spending significantly less time in the TMT side versus the controls. In summary, this study demonstrates that the classical interpretation of some unconditioned fear or anxiety tests could be misleading when animals are under the influence of drugs that might induce other competing behaviours.
A brief survey of benchmark usage in the architecture community

Benchmarking has been the staple of experimental research in computer architecture. In this familiar technique, the performance of the system is measured for a set of programs, or benchmarks, that are executed on the actual system or a simulation of the system. The benchmarks are believed to be either representative of the intended workload of the system or capable of providing insight into the range of performance variation of the system. It is interesting to survey the use of benchmarking in recent architecture papers. This paper presents a survey of benchmarking in the International Symposia on Computer Architecture, from 1984 to 1990, focusing on papers addressing processor and memory system design issues for single-CPU (uniprocessor) systems. Uniprocessor research was chosen because it experienced rapid growth during that period and it currently has the most-mature benchmark sets (i.e., SPEC [1]). Benchmarking appeared in the papers in various forms such as trace driven simulation, detailed simulation based on executable files, microcodeassisted measurement, hardware monitoring, and software probing. The benchmarks were divided into
Persistent high risk of diarrhea among foreigners in Nepal during the first 2 years of residence.

Although numerous studies have shown that diarrhea is the most common illness occurring during the first few weeks of travel, systematic studies of the incidence of diarrhea during long-term residence in developing countries have not been performed. We conducted a cohort study of the incidence and etiology of diarrhea among 77 expatriate adults who had lived in Nepal for <2 years. Persons were followed prospectively for up to 1 year (mean, 9 months). The incidence of diarrhea during the surveillance period was 3.3 episodes of diarrhea per person per year, or 0.27 episodes per person per month. The annual attack rate of specific pathogens was 42% for enterotoxigenic Escherichia coli, 32% for Cyclospora species, 16% for Giardia lamblia, 16% for Shigella species, 10% for Campylobacter species, > or =10% for rotavirus, and 6% for Entamoeba histolytica. This study suggests that adult persons from developed countries who move to developing countries such as Nepal remain at high risk for diarrhea during their first 2 years of residence.
The solution structure of eglin c based on measurements of many NOEs and coupling constants and its comparison with X‐ray structures

A high‐precision solution structure of the elastase inhibitor eglin c was determined by NMR and distance geometry calculations. A large set of 947 nuclear Overhauser (NOE) distance constraints was identified, 417 of which were quantified from two‐dimensional NOE spectra at short mixing times. In addition, a large number of homonuclear 1H‐1H and heteronuclear 1H‐15N vicinal coupling constants were used, and constraints on 42 χ1 and 38 ϕ angles were obtained. Structure calculations were carried out using the distance geometry program DG‐II. These calculations had a high convergence rate, in that 66 out of 75 calculations converged with maximum residual NOE violations ranging from 0.17 Å to 0.47 Å. The spread of the structures was characterized with average root mean square deviations () between the structures and a mean structure. To calculate the unbiased toward any single structure, a new procedure was used for structure alignment. A canonical structure was calculated from the mean distances, and all structures were aligned relative to that. Furthermore, an angular order parameter S was defined and used to characterize the spread of structures in torsion angle space. To obtain an accurate estimate of the precision of the structure, the number of calculations was increased until the and the angular order parameters stabilized. This was achieved after approximately 40 calculations. The structure consists of a well‐defined core whose backbone deviates from the canonical structure ca. 0.4 Å, a disordered N‐terminal heptapeptide whose backbone deviates by 0.8–12 Å, and a proteinase‐binding loop whose backbone deviates up to 3.0 Å. Analysis of the angular order parameters and inspection of the structures indicates that a hinge‐bending motion of the binding loop may occur in solution. Secondary structures were analyzed by comparison of dihedral angle patterns. The high precision of the structure allows one to identify subtle differences with four crystal structures of eglin c determined in complexes with proteinases.
Met5‐enkephalin is localized within axon terminals in the subfornical organ: Vascular contacts and interactions with neurons containing gamma‐aminobutyric acid

Met5‐enkephalin inhibits sodium and water excretion and antagonzes the central actions of angiotensin II in subfornical organ of rat brain. We examined the ultrastructural basis for enkephalin modulation in this circumventricular region. Additionally, we examined the possibility that there might be cellular sites for functional interactions involving Met5‐enkephalin and gamma‐aminobutyric acid (GABA), a known inhibitory transmitter throughout the central nervous system. Met5‐enkephalin and GABA were indentified in single coronal sections through the subfornical organ using immunoperoxidase and silver‐enhanced immunogold labeling methods, repectively, Enkephalin‐like immunoreactivity was most prominently localized within axon terminals. These were distributed primarily in the central, highly vascular, regions of the subfornical organ. Enkephalinlabeled terminals were apposed to the basement membranes of fenestrated capillaries and also formed symmetric, inhibitory type synapses with neurons. In terminals associated with either blood vessels or neurons, the enkephalin immunoreactivity was enriched in large (80–150nm) dense core vesicles. The immunoreactive vesicles were usually located within portions of the axon in close proximity to astrocytic processes. In contrast, smaller vesicles in the same terminals were more often aggregated near the basement membrane of the capillaries and the active zone of the synape. The targets of enkephalin‐immunoreactive terminals were either unlabeled or GABA‐labeled dendrites of local neurons. Enkephalin was also co‐localized with GABA in perikarya and in axons terminals. Terminals containing only GABA were far more abundant than those containing enkephalin or enkephalin and GABA. GABA‐immunoreactive terminals formed symmetric synapses on unlabeled dendrites some of which also received convergent input from terminals containing enkephalin. Additionally, the enkephalin‐immunoreactive terminals were closely apposed to GABA‐labeled and unlabedled terminals. These results suggest sites for nonsynaptic release of Met5‐enkephalin from dense core vesicles in contact with astrocyes near blood vessels and synaptic complexes in the rat subfornical organ. Moreover, the observed dual localization and pre‐and postsynaptic associations between neurons containing Met5‐enkephalin and GABA indicate that inhibitory effects of opioids in the subfornical organ may be mediated or potentiated by GABA. Wiley‐Liss, Inc.
Histological evaluation of healing and revascularization of the subepithelial connective tissue graft.

BACKGROUND The goal of this investigation was to histologically evaluate the healing and revascularization of the subepithelial connective tissue graft in dogs. METHODS Six beagle dogs were used in this study. Recession defects were surgically created on maxillary left P2 and right P2, and maxillary and mandibular left central and lateral incisors. The defects were left untreated for 35 days. After elevating a split thickness flap, the graft was harvested from the palate and placed over the denuded root surfaces. The flap was then coronally repositioned and sutured. Three dogs provided the specimens for 7- and 14-day time points and 3 dogs for 28- and 60-day time points. The animals were sacrificed and the blocks obtained were divided in half. One half was processed following the Spalteholtz method and the other was processed for routine histologic examination. RESULTS At 7 days, a clot was present at the demarcation zones and it was more organized at 14 days. At 28 days, the junctional epithelium was formed and the demarcation zones could not be delineated. At 60 days, the oral epithelium had regained its normal appearance. The attachment of the graft to the root surface was mediated by a combination of epithelial downgrowth and connective tissue attachment. Minimal new bone and cementum formation was observed. The vascularization of the graft at 7 days originated from the periodontal plexus and the overlying flap. At 14 days, the graft was completely vascularized. At 28 and 60 days, normal vascularization was present. CONCLUSIONS The vascularization of the connective tissue graft originates from the periodontal plexus, the supraperiosteal plexus, and the overlying flap. The attachment of the graft to the root surface appears to be mediated by a combination of epithelial downgrowth and connective tissue attachment. There is little potential for new cementum and new bone formation.
Spontaneous Remission in Congenital Leukemia AML-M1 with Pericardial Effusion

Congenital leukemia is a very rare malignancy of childhood with a poor prognosis. The incidence is nearly 1 in 5 million live births. The majority of cases are acute myeloblastic leukemia with trisomy. Clinical manifestations are usually leukocytosis, petechia, ecchymosis, cutaneous nodules, hepatosplenomegaly and central nervous system symptoms. 23-days old girl was presented with complaints of maculopapular dermatitis and hepatosplenomegaly diagnosed as AML M1. During the follow-up period massive pericardial effusion was detected. This case is presented due to emphasize the rare association of pericardial effusion with congenital leukemia without trisomy and spontaneous remission of leukemia that was occasionally appear in the literature.
Assimilating satellite microwave radiance measurements over the Antarctic

As there are few in situ observations in and around Antarctica, it is important to assess how assimilating remotely-sensed observations, such as satellite-observed radiances, can fill this observational gap. Thus, a month-long study was conducted over the Antarctic to examine forecast and analysis sensitivity to the assimilation of microwave radiance measurements. Several experiments were configured to quantify the impact of radiance data assimilation (DA) and explore different approaches of radiance bias correction (BC). DA was performed using WRFDA’s three-dimensional variational (3DVAR) algorithm, and the analyses initialized 72-hr WRF-ARW forecasts. The results demonstrate the critical importance of properly bias correcting raw radiance observations. When assimilating radiances using a “cold start” BC technique, forecasts and analyses were degraded compared to those from a parallel experiment that only assimilated conventional (i.e., non-radiance) observations. However, when BC parameters were “spun-up” for several months before the assimilation period, radiance DA yielded forecast and analysis improvements compared to when only conventional observations were assimilated.
Ureteroscopic Laser Lithotripsy versus Ballistic Lithotripsy for Treatment of Ureteric Stones: A Prospective Comparative Study

Objectives: This study was undertaken to compare the results of laser (Ho:YAG) and pneumatic (ballistic) intracorporeal lithotripsy for ureteric calculi in terms of efficacy, safety and complications. Methods: 55 patients having ureteric calculus were randomly allocated into pneumatic lithotripsy (PL) and laser lithotripsy (LL) groups. Swiss lithoclast was used for PL (3 atm pressure and 12 Hz frequency) and the VersaPulse PowerSuite was used for LL. Appropriate statistical tests were applied. Results: 30 patients (34 stones) were treated with LL and 25 patients (25 stones) with PL. Both groups were comparable in profile. Mean lithotripsy time was 24.03 ± 9.51 min in the LL group and 19.80 ± 4.44 min in the PL group (p = 0.027). The immediate stone clearance rate was higher in the LL group (p = 0.001), but it was comparable at 4 weeks (p = 0.097). Stone migration occurred in 16% of cases in the PL group. No major complication was observed in either group. Conclusions: We conclude that both laser and pneumatic energies are effective and safe for intracorporeal lithotripsy. Laser lithotripsy takes more time but provides earlier stone-free status.
APPIC : Finding The Hidden Scene Behind Description Files for Android Apps

Today one of the greatest abundance of applications (apps) are those found on mobile devices. The procedure to download an app has never been easier. The user will first find the desired app within an app market such as the Google Play. Once the user finds the desired app normally a description is given. This description will give the user information on what they are trying to purchase. The user will then download this new piece of software based off of the trust that the description given is correct. This brings to light the new threats that there are chances the descriptions could be misleading. This paper will present the idea of APPIC to solve such issue. APPIC is a framework that can automatically extract main theme (tags) from both the description pages and permission file. By further checking the similarity of these tags, we can verify the validity of the description. In the APPIC the core component is topic modeling. Using different topic models, the APPIC can verify different contents within an app market such as comments and screenshots. For this paper, we will discuss the two main methods used in the APPIC which are latent dirichlet allocation (LDA) and partially labeled dirichlet allocation (PLDA). During the testing phase the APPIC will use different parameters, topics, models and categories. We have achieved on average 88.1% precision of the app description classification, and on average a 76.5% accuracy of the app permission classification. Therefore, the APPIC can largely reduce the number of misleading descriptions within the app markets.
Agent‐based secure routing for underwater acoustic sensor networks

The underwater networks have severe security implications and are vulnerable to various types of attacks such as selective forwarding, wormhole, and sinkhole. Neighbor discovery, a fundamental requirement for routing is vulnerable to wormhole attack, which enables false neighbor acceptance, thereby degrading the routing performance. The proposed agent‐based secured routing scheme enhances the quality of service by discovering the wormhole resilient secure neighbors and route the information through the secure path. This scheme uses 4 agencies, namely, security, routing, underwater gateway, and vehicle, which are embedded with static and mobile agents. (1) Agents in security agency of a node discover secured neighbors by using the direction of arrival estimation and authentication, (2) agents in routing agency of a node establish secured routes from source to surface gateway, (3) agents in Underwater Gateway Agency communicate with Autonomous Underwater Vehicles (AUVs) and underwater nodes for key distribution, and (4) vehicle traversing agency in AUV coordinates with Underwater Gateway Agency for changing AUVs traversal to cover the isolated network area. The proposed scheme depicts the improved performance compared to basic neighbor discovery and channel aware routing protocol in terms of failure detection, energy consumption, and overheads.
A stakeholder perspective within software engineering projects

Successful software engineering projects result when stakeholders care about the issues and know that their ideas, opinions and contributions are valued. There is evidence to suggest that the successful delivery of software engineering projects is directly related to the way in which the project manager involves stakeholders in the decision making process within the various stages of the project. We will examine and discusses the extent to which stakeholders participate and to what degree stakeholders influence the project management process.