Miracle-dz/UniFAR-FTUs huggingface dataset:
Choosing among alternative pasts

The main problem with testing concurrent programs is their non-determinism: two executions of such a program may yield different results. The traditional solution is to identify and examine the race conditions. A different approach is that of generating different interleavings at runtime using embedded sleep statements. Advantages of this approach over the traditional one include its ability to identify more problems, and the absence of the false alarms. This paper proposes a totally different technique for the generation of interleavings. Operations on shared variables are tracked. Every time a shared variable is read, the read value is chosen among the values that the variable could hold in some interleaving consistent with the past observed events. The event timing restrictions are then updated based on the value chosen. The problem of identifying legal read values is far from simple due to the fact that past value substitutions affect future ones. Our solution is computationally intensive and, therefore, impractical as is. However, insights gained from it lead to practical heuristics for operating the embedded sleep statements.
Investigation and Modeling of Hot Carrier Effects on Performance of 45- and 55-nm NMOSFETs With RF Automatic Measurement

Effects of hot carriers on dc and RF reliabilities for both 45- and 55-nm negative metal-oxide-semiconductor field-effect transistors with in-line ground-signal-signal-ground test-pad structures were investigated in detail. The investigations were evaluated by an RF automatic testing system with a proprietary control program in Agilent's Integrated Circuit Characterization and Analysis Program software. After a hot carrier stress, we found that the increase in Cgs is larger than the decrease in Cgd for 55- and 45-nm devices, and the difference increases as the process technology keeps advancing. Thus, the degradations of cutoff frequency fT and maximum oscillation frequency fmax are dependent on transconductance gm and gate capacitance Cgg (= Cgs + Cgd) for 45- and 55-nm devices. This is different than many conventional studies that used low-frequency equipment. We propose a surface channel resistance model to comprehensively interpret the observations and verify it by the slope changes in the curves of measured fT versus gm.
Population Structure and Resistance Genes in Antibiotic-Resistant Bacteria from a Remote Community with Minimal Antibiotic Exposure

ABSTRACT In a previous study, we detected unexpectedly high levels of acquired antibiotic resistance in commensal Escherichia coli isolates from a remote Guaraní Indian (Bolivia) community with very low levels of antibiotic exposure and limited exchanges with the exterior. Here we analyzed the structure of the resistant E. coli population from that community and the resistance mechanisms. The E. coli population (113 isolates from 72 inhabitants) showed a high degree of genetic heterogeneity, as evidenced by phylogenetic grouping (77% group A, 10% group B1, 8% group D, 5% group B2) and genotyping by randomly amplified polymorphic DNA (RAPD) analysis (44 different RAPD types). The acquired resistance genes were always of the same types as those found in antibiotic-exposed settings [blaTEM, blaPSE-1, catI, cmlA6, tet(A), tet(B), dfrA1, dfrA7, dfrA8, dfrA17, sul1, sul2, aphA1, aadA1, aadA2, aadA5, aadB, and sat-1]. Class 1 and class 2 integrons were found in 12% and 4% of the isolates, respectively, and harbored arrays of gene cassettes similar to those already described. The cotransferability of multiple-resistance traits was observed from selected isolates and was found to be associated with resistance conjugative plasmids of the F, P, and N types. Overall, these data suggest that the resistance observed in this remote community is likely the consequence of the dissemination of resistant bacteria and resistance genes from antibiotic-exposed settings (rather than of an independent in situ selection) which involved both the clonal expansion of resistant strains and the horizontal transfer/recombination of mobile genetic elements harboring resistance genes.
A three‐factor analytic model of the MADRS in geriatric depression

Major depression is a heterogeneous disorder, perhaps comprising several clinical subtypes or subgroups of symptoms. This study examined whether items on the Montgomery‐Åsberg Depression Rating Scale (MADRS) form distinct symptom subgroups among geriatric depressive patients that might form the basis of new outcome measures for tracking treatment effects.
Algebraic Synthesis of Forest Scenarios From Multibaseline PolInSAR Data

In this paper, a new methodology is proposed for the analysis of forested areas basing on multipolarimetric multibaseline synthetic aperture radar (SAR) surveys. Such a methodology is based on three hypotheses: 1) statistical uncorrelation of the different scattering mechanisms (SMs), such as ground, volume, and ground-trunk scattering; 2) independence of volumetric and temporal coherence losses of each SM on the choice of the polarimetric channel; and 3) invariance (up to a scale factor) of the average polarimetric signature of each SM with respect to the choice of the track. Under these hypotheses, the data covariance matrix can be expressed as a Sum of Kronecker Products, after which it follows that K SMs are uniquely identified by K (K - 1) real numbers. This result provides the basis to perform SM separation by employing not only model-based approaches, generally retained in literature but also model-free and hybrid approaches, while yielding the best Least Square solution given the hypothesis of K SMs. It will be shown that this approach to SM separation is consistent with the inversion procedures usually exploited in single-baseline polarimetric SAR interferometry. Experimental validation of this methodology is provided on the basis of the P-band data set relative to the forest site of Remningstorp, Sweden, acquired by German Aerospace Center's E-SAR airborne system in the framework of the European Space Agency campaign BioSAR.
Lack of Significant Changes on Magnetic Resonance Scans Before and After 2 Weeks of Daily Left Prefrontal Repetitive Transcranial Magnetic Stimulation for Depression

Repetitive transcranial magnetic stimulation (rTMS) is a new technology for exploring brain function. With this method, a small electromagnet is placed on the scalp; by activating and deactivating it, nerve cells in the underlying superficial cortex are depolarized. Several studies have found that prefrontal rTMS has potential efficacy in treating depression, and this technology, in addition to being a research tool, may soon play a role in psychiatric practice. Thus, establishing the safety of this technology is important and has been studied insufficiently. The authors performed T1-weighted three-dimensional volumetric magnetic resonance (MR) imaging on 22 depressed adults (15 active, 7 control) before and after they participated in a 2-week double-blinded, placebo-controlled trial of daily left prefrontal rTMS for the treatment of depression (a total of 16,000 stimuli). Seventeen patients also had paired T2-weighted scans. In a blinded manner, MR scans were qualitatively and quantitatively assessed for structural changes. No qualitative structural differences were observed before and after treatment. In addition, volumetric analysis of the prefrontal lobe showed no changes in the 2 weeks of the study. In conclusion, 10 days of daily prefrontal rTMS at these intensities and frequencies does not cause observable structural changes on MR scans in depressed adults.
Articulated Human Body: 3D Pose Estimation Using a Single Camera

We address how human pose in 3D can be tracked from a monocular video using a probabilistic inference method. Human body is modeled as a number of cylinders in space, each with an appearance facet as well as a pose facet. The appearance facets are acquired in a learning phase from some beginning frames of the input video. On this the visual hull description of the target human subject constructed from multiple images is found to be instrumental. In the operation phase, the 3D pose of the target subject in the subsequent frames of the input video is tracked. A bottom-up framework is used, which for any current image frame extracts firstly the tentative candidates of each body part in the image space. The human model, with the appearance facets already learned, and with the pose entries initialized with those for the previous image frame, is then brought in under a belief propagation algorithm, to establish correlation with the above 2D body part candidates while enforcing the proper articulation between the body parts, thereby determining the 3D pose of the human body in the current frame. The tracking performance on a number of monocular videos is shown.
Uveal melanoma cell growth is inhibited by aminoimidazole carboxamide ribonucleotide (AICAR) partially through activation of AMP-dependent kinase.

PURPOSE To evaluate the effects and mechanism of aminoimidazole carboxamide ribonucleotide (AICAR), an AMP-dependent kinase (AMPK) activator, on the growth of uveal melanoma cell lines. METHODS Four different cell lines were treated with AICAR (1-4 mM). Cell growth was assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium (MTT) assay. Cell cycle analysis was conducted by flow cytometry; additionally, expression of cell-cycle control proteins, cell growth transcription factors, and downstream effectors of AMPK were determined by RT-PCR and Western blot. RESULTS Aminoimidazole carboxamide ribonucleotide inhibited cell growth, induced S-phase arrest, and led to AMPK activation. Aminoimidazole carboxamide ribonucleotide treatment was associated with inhibition of eukaryotic translation initiation factor 4E-BP1 phosphorylation, a marker of mammalian target of rapamycin (mTOR) pathway activity. Aminoimidazole carboxamide ribonucleotide treatment was also associated with downregulation of cyclins A and D, but had minimal effects on the phosphorylation of ribosomal protein S6 or levels of the macroautophagy marker LC3B. The effects of AICAR were abolished by treatment with dipyridamole, an adenosine transporter inhibitor that blocks the entry of AICAR into cells. Treatment with adenosine kinase inhibitor 5-iodotubericidin, which inhibits the conversion of AICAR to its 5'-phosphorylated ribotide 5-aminoimidazole-4-carboxamide-1-D-ribofuranosyl-5'-monophosphate (ZMP; the direct activator of AMPK), reversed most of the growth-inhibitory effects, indicating that some of AICAR's antiproliferative effects are mediated at least partially through AMPK activation. CONCLUSIONS Aminoimidazole carboxamide ribonucleotide inhibited uveal melanoma cell proliferation partially through activation of the AMPK pathway and downregulation of cyclins A1 and D1.
Experimental Validation of a Nested Polymerase Chain Reaction Targeting the Genetic Element ISMAP02 for Detection of Mycobacterium Avium Subspecies Paratuberculosis in Bovine Colostrum

Colostrum samples experimentally inoculated with Mycobacterium avium subsp. paratuberculosis (MAP; strain K-10) at increasing concentrations between 1 × 101 and 1 × 109 cells/ml were tested for recovery of MAP DNA using a nested ISMAP02 target polymerase chain reaction initially developed for detecting MAP DNA in fecal samples. The following detection rates were achieved for sample replicates inoculated with unsonicated MAP pure stock: 100% between 1 × 107 and 1 × 109 cells/ml, 75% between 1 × 103 and 1 × 106 cells/ml, and 50% between 1 × 101 and 1 × 102 cells/ml replicates. Detection rates achieved for the colostrum sample replicates inoculated with sonicated MAP cell suspension were 75% for 1 × 109 cells/ml, 100% between 1 × 107 and 1 × 108 cells/ml, 75% for 1 × 106 cells/ml, 0 for 1 × 104 cells/ml, and 25% between 1 × 101 and 1 × 103 cells/ml. When negative control colostrum samples were tested, 16 of 18 (89%) samples were correctly detected as negative for MAP DNA using the current assay. In conclusion, the MAP DNA detection rates of the present assay improved with increasing concentrations of MAP in the colostrum sample replicates, although MAP DNA was also detected in 2 of 18 (11%) negative control samples, suggesting an undefined technical problem with the assay or, perhaps, sample contamination during preparation. Overall, the present findings suggest a potential role of the proposed polymerase chain reaction assay to detect MAP in colostrum. However, adoption of this test for use in routine screening of field colostrum for MAP awaits findings from an ongoing field validation study.
Posttranslational Heterogeneity of Bone Alkaline Phosphatase in Metabolic Bone Disease

Bone alkaline phosphatase is a marker of osteoblast activity. In order to study the posttranscriptional modification (glycosylation) of bone alkaline phosphatase in bone disease, we investigated the relationship between mass and catalytic activity of bone alkaline phosphatase in patients with osteoporosis and hyperthyroidism. Serum bone alkaline phosphatase activity was measured after lectin precipitation using the Iso-ALP test kit. Mass concentration of bone alkaline phosphatase was determined with an immunoradiometric assay (Tandem-R Ostase). In general, serum bone alkaline phosphatase mass and activity concentration correlated well. The activity : mass ratio of bone alkaline phosphatase was low in hyperthyroidism. Activation energy of the reaction catalysed by bone alkaline phosphatase was high in osteoporosis and in hyperthyroidism. Experiments with neuraminidase digestion further demonstrated that the thermodynamic heterogeneity of bone alkaline phosphatase can be explained by a different glycosylation of the enzyme.
Negative Social Reactions to Assault Disclosure as a Mediator between Self-Blame and Posttraumatic Stress Symptoms Among Survivors of Interpersonal Assault

The type of causal attributions offered for traumatic life events has been documented as a potential vulnerability factor for posttraumatic stress disorder (PTSD). However, few investigations have sought to identify the mechanisms by which such explanations are associated with greater posttraumatic distress. One possible factor that may account for the relationship between maladaptive attributional tendencies and PTSD symptoms is the quality of social reactions received from one’s social network upon disclosure. The aim of the present study was to examine the relationship between self-blaming attributions provided for traumatic events, negative social reactions, and PTSD symptom severity. Undergraduate psychology students (N = 68), who reported previously experiencing interpersonal assault, completed measures assessing their attributions for their assault and the quality of reactions received from members of their social network upon disclosure. Results from a statistical mediational analysis suggest that a self-blame may be associated with poorer psychological adjustment by virtue of negative social reactions. Results of this study further our understanding of risk and resilience among assault survivors and may have significant implications for treatment interventions for individuals with PTSD.
Self-assembly of amphiphilic Janus dendrimers into mechanically robust supramolecular hydrogels for sustained drug release.

Compounds that can gelate aqueous solutions offer an intriguing toolbox to create functional hydrogel materials for biomedical applications. Amphiphilic Janus dendrimers with low molecular weights can readily form self-assembled fibers at very low mass proportion (0.2 wt %) to create supramolecular hydrogels (G'≫G'') with outstanding mechanical properties and storage modulus of G'>1000 Pa. The G' value and gel melting temperature can be tuned by modulating the position or number of hydrophobic alkyl chains in the dendrimer structure; thus enabling exquisite control over the mesoscale material properties in these molecular assemblies. The gels are formed within seconds by simple injection of ethanol-solvated dendrimers into an aqueous solution. Cryogenic TEM, small-angle X-ray scattering, and SEM were used to confirm the fibrous structure morphology of the gels. Furthermore, the gels can be efficiently loaded with different bioactive cargo, such as active enzymes, peptides, or small-molecule drugs, to be used for sustained release in drug delivery.
Computational Study of Intramolecular Heterocyclic Ring Formation with Cyclic Phosphazenes

Polyphosphazenes, because of their unique properties, have generated many opportunities to explore a variety of applications. These applications include areas such as biomedical research (e.g. drug delivery) and material science (e.g. fire-resistant polymers). Phosphazenes potentially have more variations then benzene analogues because of different substitution patterns. Here we present A computational study of the chemical modifications to a group of cyclic phosphazenes mainly hexachlorophosphazene (PNCl2)3. This study focuses on the relative energies of reactivity of hexachlorophosphazene to understand their geometry and the complexes they likely form. We compare diols, amino alcohols, and diamines with a carbon linker of 1-7 atoms. These heteroatom chains are attached to a single phosphorus atom or adjoining phosphorus atoms to form ring structures of geminal, vicinal (cis), and vicinal (trans) moieties. We find that the reactivities of “heteroatom caps” are predicted to be O,O (diol) > N,O (amino alcohol) > N,N (diamine). These results can be used to predict energetics and thus the stability of new compounds for biomedical and industrial applications.
A sure-fired way to choose smoothing parameters in ill-conditioned inverse problems

Regularisation methods for the solution of inverse problems are well known although the theoretical study of their performance especially in image processing contexts is not well advanced. What is also much less resolved is smoothing or penalty parameter estimation. We describe a general procedure for estimation of auxiliary finite dimensional parameters in ill-conditioned inverse problems. The method is applicable to nonlinear problems, involves no approximations but offers computational advantages over cross validation and maximum likelihood.
Interplay between Drosophila Bloom's syndrome helicase and Ku autoantigen during nonhomologous end joining repair of P element-induced DNA breaks

P transposable elements in Drosophila are mobilized via a cut-and-paste mechanism. The broken DNA ends generated during transposition can be repaired via the homology-directed synthesis-dependent strand annealing or by nonhomologous end joining (NHEJ). Genetic studies have demonstrated an interaction between the gene (mus309, for mutagen-sensitive) encoding the Drosophila Bloom's syndrome helicase homolog (DmBLM) and the Ku70 gene, which is involved in NHEJ. We have used RNA interference (RNAi) to knock down expression of DmBLM and one or both of the Drosophila Ku subunits, DmKu70 or DmKu80. Our results show that upon reduction of DmKu, an increase in small deletions (1–49 bp) and large deletions (≥50 bp) flanking the site of P element-induced breaks is observed, and a reduction in large deletions at these sites is found upon reduction of DmBLM. Moreover, double RNAi of DmKu and DmBLM results in an increase in small deletions characteristic of the DmKu RNAi and also partially suppresses the reduction in repair efficiency observed with DmKu RNAi. These results suggest that there are DNA double-strand break recognition and/or processing events involving DmKu and DmBLM that, when eliminated by RNAi, lead to deletions. Finally, these results raise the possibility that, unlike the situation in mammals, where BLM appears to function exclusively in the homologous repair pathway, in Drosophila, DmBLM may be directly involved in, or at least influence the double-strand break recognition that leads to the NHEJ repair pathway.
3D multi-stacking of thin dies based on TSV and micro-inserts interconnections

This paper is dedicated to the full development of several technological modules mandatory for 3-D multiple die stacking. This includes technologies such as thinning, Through Silicon Vias (TSV) and dies interconnection. A via last approach was chosen to be compatible with die integration coming from various foundries where design, die thickness and contact pad metallurgy are predefined. The interconnection between each die is based on chip on wafer bonding and micro-inserts technology. Small spikes of Ni are formed at the interconnection point between the two circuits. The approach allows a very narrow connection (less than 10 μm of interface) and do not necessitate an underfill. A test vehicle which allows characterizing the required technologies has been designed and manufactured. It consists of 50 μm thick dies including TSV and contact lines on both sides. These dies are stacked on silicon interconnection network enabling to extract electrical signal. The electrical continuity through the stacking was tested from the substrate thanks to Daisy Chain. Finally, these technologies were implemented in a SimCard prototype. The test vehicle and final prototype will be fully described in this paper. A technical focus will be done on the most important process steps for the 3D integration which include vias last integration, micro-bumping and thin die stacking. Several electrical Kelvin structures were measured from the substrate to estimate the contact resistance through micro-inserts and TSV and results will be presented and commented.
A tumor host range selection procedure identifies p150sal2 as a target of polyoma virus large T antigen

Cancer cells may undergo loss or alterations in functions that certain viruses normally target to promote virus replication. Virus mutants that have lost the targeting function(s) should be able to grow in such cancer cells but not in normal cells. A “tumor host range” (t-hr) selection procedure has been devised and applied to polyoma virus based on this rationale. Studies of one t-hr mutant have led to the identification of the mSal2 gene product (p150sal2) as a binding partner of the large T antigen. mSal2 encodes a multizinc finger protein and putative transcription factor homologous to the Drosophila homeotic gene Spalt. The t-hr mutant encodes an altered large T protein that fails to interact with p150sal2 and is defective in replication and tumor induction in newborn mice.
Patient Medication Adherence and Physician Prescribing among Congestive Heart Failure Patients of Yemen

Congestive heart failure has been associated with high morbidity and mortality requiring hospitalisation and is further complicated by noncompliance and under prescriptions. We aim to determine medication adherence and percentage deviation among Asians population in general and Yemenis in particular. A cross-sectional, prospective observational study with purposive sampling was conducted at two cardiac outpatient centers in 70 congestive heart failure patients for a period of 3 months. An Arabic translated Morisky 4 item scale assessed the adherence of patients. Deviation in prescribing was determined by chart review. All 70 patients had mean age of 56.6±16 years. Morisky 4 item scale predicted low adherence (n=33; 47.1%) and overall nonadherencerate (n=38; 54.2%) was slightly higher than adherence. Percentage nonadherence versus adherence was high with diuretics (53 vs. 46%) and, digoxin (40 vs. 29%). The adherence percentage of angiotensin receptor blockers (9%) and beta blockers (8%) was low. Diuretics were the most prescribed drugs (n=69; 99%), followed by angiotensin converting enzyme inhibitors (n=51; 73%), cardiac glycoside (n=48; 69%), few patients were on angiotensin receptor blockers (n=8; 11%) and (n=9; 13%) beta blockers. The maximum prescribing rate deviation was seen with angiotensin receptor blockers (−89%) and beta blockers (−87%) followed by nitrates (−77%). Digoxin (−31%) and angiotensin converting enzymes (−27%) deviated comparatively less. Prescribing as well as utilisation rates generally were low resulting in nonachievement of therapeutic goals which could be resolved using multimodel approach.