Miracle-dz/UniFAR-FTUs huggingface dataset:
Just: Safe Unknown Types in Java-like Languages

Most mainstream object-oriented languages, like C++, Java and C#, are statically typed. In recent years, untyped languages, in particular scripting languages for the web, have gained a lot of popularity notwithstanding the fact that the advantages of static typing, such as earlier detection of errors, are widely accepted. We think that one of the main reasons for their widespread adoption is that, in many situations, the ability of ignoring types can be handy to write simpler and more readable code. We propose an extension of Java-like languages which allows developers to forget about typing in strategic places of their programs without losing type-safety. That is, we allow programmers to write simpler code without sacriﬁcing the advantages of static typing. This is achieved by means of inferred type constraints. These constraints describe the implicit requirements on untyped code to be correctly invoked. This ﬂexibility comes at a cost: ﬁeld accesses and method invocations on objects of unknown types are less eﬃcient than regular ﬁeld accesses and method invocations. Also, our type system is currently more restrictive than it should be; its extension is the subject of ongoing work. However, the novel approach presented here is quite interesting on its own, as it supports separate compilation and there is zero runtime overhead on code which does not take advantage of the new features. We have implemented our approach on a small, yet signiﬁcant, Java subset.
Contribution of Dual Fluorescein and Indocyanine Green Angiography to the Appraisal of Presumed Tuberculous Chorioretinitis in a Non-endemic Area

Purpose: To assess the respective involvement of retina versus choroid in presumed ocular tuberculosis (POT) in a non-endemic area using dual fluorescein (FA) and indocyanine green angiography (ICGA). Methods: We retrospectively analyzed cases diagnosed with POT at the Centre for Ophthalmic Specialized Care, Lausanne, Switzerland. Angiography signs were quantified using an established dual FA and ICGA scoring system for uveitis. Results: Out of 1739 uveitis patients visited from 1995 to 2014, 53 (3%) were diagnosed with POT; of whom 28 patients (54 eyes) had sufficient data available to be included in this study. Of 54 affected eyes, 39 showed predominant choroidal involvement, 14 showed predominant retinal involvement and one had equal retinal and choroidal scores. Mean angiographic score was 6.97 ± 5.08 for the retina versus 13.48 ± 7.06 for the choroid (P < 0.0001). For patients with sufficient angiographic follow-up after combined anti-tuberculous and inflammation suppressive therapy, mean FA and ICGA scores decreased from 6.97 ± 5.08 to 3.63 ± 3.14 (P = 0.004), and 13.48 ± 7.06 to 7.47 ± 5.58 (P < 0.0001), respectively. Conclusion: These results represent the first report of the respective contributions of retinal and choroidal involvement in POT. Choroidal involvement was more common, for which ICGA is the preferred examination. In cases of compatible uveitis with positive results of an interferon-gamma release assay, particularly in a region that is non-endemic for TB, dual FA and ICGA should be performed to help establish the diagnosis of ocular tuberculosis and improve follow-up.
Ubiquitination Mediated by the Npi1p/Rsp5p Ubiquitin-protein Ligase Is Required for Endocytosis of the Yeast Uracil Permease (*)

Uracil uptake by Saccharomyces cerevisiae is mediated by the FUR4-encoded uracil permease. This permease undergoes endocytosis and subsequent degradation in cells subjected to adverse conditions. The data presented here show that uracil permease also undergoes basal turnover under normal growth conditions. Both basal and induced turnover depend on the essential Npi1p/Rsp5p ubiquitin-protein ligase. Epitope-tagged ubiquitin variants have been used to show that uracil permease is ubiquitinated in vivo. The ubiquitin-permease conjugates that are readily demonstrated in wild type cells were barely detectable in npi1 mutant cells, indicating that uracil permease may be a physiological substrate of the Npi1p ubiquitin ligase. The lack of ubiquitination of the permease in npi1 cells resulted in an increase in active, i.e. plasma membrane-located, permease, suggesting that there is a direct relationship between ubiquitination and removal of the permease from the plasma membrane. The accumulation of ubiquitin-permease conjugates in thermosensitive act1 mutant cells, deficient in the internalization step of endocytosis is consistent with this idea. On the other hand, the degradation of uracil permease does not require a functional proteasome since the permease was not stabilized in either pre1 pre2 or cim3 and cim5 mutant cells that have impaired catalytic (pre) or regulatory (cim) proteasome subunits. In contrast, both basal and stress-stimulated turnover rates were greatly reduced in pep4 mutant cells having defective vacuolar protease activities. We therefore propose that ubiquitination of uracil permease acts as a signal for endocytosis of the protein that is subsequently degraded in the vacuole.
A Domain-specific Modelling Language for Clinical Pathways in the Realm of Multi-perspective Hospital Modelling

To increase the quality and decrease costs of medical care provision, hospitals apply clinical pathways (CPs) to ‘model’ and manage their processes. Conceptual models of CPs should foster communication between hospital stakeholders, serve as an instrument for quality assurance and optimisation of resource usage, and a foundation for the (re-)design of hospitals’ action and information system (IS). However, existing approaches to CPs’ modelling suffer from simplifications and a low level of domain-specific semantics. In addition, they focus mainly on processes and neglect other aspects relevant to a comprehensive management of hospitals. We argue that to realise the potential benefits of CPs, a comprehensive modelling method accounting for peculiarities of hospitals’ action system and IS is required. The core of such a method should be a Domain-Specific Modelling Language for CPs presented in this paper.
Assessing the Feasibility of Forming a Common Currency Area among D-8 Group Members: G-PPP Method

This paper examines the feasibility of forming a common currency area between D-8 group members by testing Purchasing Power Parity (PPP) and Generalized Purchasing Power Parity (G-PPP) theories over the period of 1993–2010. According to the results of Johansen Fisher Panel Cointegration method and Johansen Multivariate Cointegration method, the weak form of PPP theory and GPPP theory exist. It shows that these countries tend to be affected by similar shocks. Also the macroeconomic fundamentals that determine real exchange rates in D-8 group members are interrelated such that bilateral real exchange rates in these countries share common stochastic trends in the long run. Therefore, the minimum precondition to form a common currency area between D-8 group members exists. A good performance of a common currency area may increase the economic integration among mentioned countries and enhances their role in international decision-making. According to the results, Pakistan is the most proper member to start a common currency area. Turkey and Malaysia's economic structure are different from other members such that they are not proper countries to inter the common currency area with other members of D-8 group.
Intranasal Immunization with Chitosan/pCAGGS-flaA Nanoparticles Inhibits Campylobacter jejuni in a White Leghorn Model

Campylobacter jejuni is the most common zoonotic bacterium associated with human diarrhea, and chickens are considered to be one of the most important sources for human infection, with no effective prophylactic treatment available. We describe here a prophylactic strategy using chitosan-DNA intranasal immunization to induce specific immune responses. The chitosan used for intranasal administration is a natural mucus absorption enhancer, which results in transgenic DNA expression in chicken nasopharynx. Chickens immunized with chitosan-DNA nanoparticles, which carried a gene for the major structural protein FlaA, produced significantly increased levels of serum anti-Campylobacter jejuni IgG and intestinal mucosal antibody (IgA), compared to those treated with chitosan-DNA (pCAGGS). Chitosan-pCAGGS-flaA intranasal immunization induced reductions of bacterial expellation by 2-3 log10 and 2 log10 in large intestine and cecum of chickens, respectively, when administered with the isolated C. jejuni strain. This study demonstrated that intranasal delivery of chitosan-DNA vaccine successfully induced effective immune response and might be a promising vaccine candidate against C. jejuni infection.
Agreement in classifying bloodstream infections among multiple reviewers conducting surveillance.

BACKGROUND Mandatory reporting of healthcare-associated infections (HAIs) is increasing. Evidence for agreement among different reviewers applying HAI surveillance criteria is limited. We aim to characterize agreement among infection preventionists (IPs) conducting surveillance for central line-associated bloodstream infection (CLABSI) with each other and as compared with simplified laboratory-based definitions. METHODS Abstracted electronic health records were assembled from inpatients with positive blood cultures at a tertiary-care Veterans Affairs (VA) hospital over a 5-year period. Identical patient records were made available to VA IPs from different facilities to report on CLABSI using their usual surveillance methods. Positive blood cultures were also evaluated using laboratory-based definitions. Standard indices of interrater agreement, expressed as a κ statistic, were computed between IPs, and between IPs and simplified laboratory-based methods. RESULTS Overall, 114 patient records were reviewed by 18 IPs, the majority of whom specified they followed National Healthcare Safety Network criteria. The overall agreement among IPs by κ statistic was 0.42 (standard error [SE], 0.06). IPs had better agreement with a simple laboratory-based definition with an average κ of 0.55 (SE, 0.05). The proportion of patient records that 18 IPs reported with CLABSI ranged from 14% to 39% (overall mean, 28% with a coefficient of variation of 25%). When simple laboratory-based methods were applied to different sets of patient records, classification was more consistent with CLABSI assigned in a proportion ranging from 36% to 42% (overall mean, 39%). CONCLUSIONS Reliability of IP-conducted surveillance to identify HAI may not be ideal for public reporting goals of interhospital comparisons.
SNAP for ArcGIS : A Planning and Educational Tool for Forest Engineers

SNAP for ArcGIS is a computer software developed to streamline harvest area analysis for spatially-explicit timber harvest scheduling and transportation planning at a project level. This planning tool uses modern scheduling and network algorithms to develop harvest schedules up to three time periods with consideration of harvesting options and costs, multiple timber products, alternative mill destinations, and road systems. SNAP for ArcGIS attempts either to maximize net present value (NPV) or minimize discounted costs of harvesting and transportation over the planning horizon, while meeting given harvest volume and acreage constraints per planning period. With SNAP for ArcGIS, the user can generate vegetation management solutions that are cost-effective and operationally feasible under given management goals and strategies. The potential users of the tool are project planners and logging engineers who have basic knowledge of timber harvest and transportation planning, silvicultural prescriptions, and geographic information systems. SNAP for ArcGIS can be also used as an educational tool in classroom, workshop, and professional training that provides students with insight into the dynamics and complexity of tactical and operational planning for timber management.
Contribution of Underlying Connective Tissue Cells to Taste Buds in Mouse Tongue and Soft Palate

Taste buds, the sensory organs for taste, have been described as arising solely from the surrounding epithelium, which is in distinction from other sensory receptors that are known to originate from neural precursors, i.e., neural ectoderm that includes neural crest (NC). Our previous study suggested a potential contribution of NC derived cells to early immature fungiform taste buds in late embryonic (E18.5) and young postnatal (P1-10) mice. In the present study we demonstrated the contribution of the underlying connective tissue (CT) to mature taste buds in mouse tongue and soft palate. Three independent mouse models were used for fate mapping of NC and NC derived connective tissue cells: (1) P0-Cre/R26-tdTomato (RFP) to label NC, NC derived Schwann cells and derivatives; (2) Dermo1-Cre/RFP to label mesenchymal cells and derivatives; and (3) Vimentin-CreER/mGFP to label Vimentin-expressing CT cells and derivatives upon tamoxifen treatment. Both P0-Cre/RFP and Dermo1-Cre/RFP labeled cells were abundant in mature taste buds in lingual taste papillae and soft palate, but not in the surrounding epithelial cells. Concurrently, labeled cells were extensively distributed in the underlying CT. RFP signals were seen in the majority of taste buds and all three types (I, II, III) of differentiated taste bud cells, with the neuronal-like type III cells labeled at a greater proportion. Further, Vimentin-CreER labeled cells were found in the taste buds of 3-month-old mice whereas Vimentin immunoreactivity was only seen in the CT. Taken together, our data demonstrate a previously unrecognized origin of taste bud cells from the underlying CT, a conceptually new finding in our knowledge of taste bud cell derivation, i.e., from both the surrounding epithelium and the underlying CT that is primarily derived from NC.
Detection of questions in Berber language using prosodic features

This paper focuses on the acquisition of the tonal and prosodic structure of affirmative and question sentences in Berber language. The study on the prosodic differences between these two types of sentences in Berber language, the detection and classification of sentence type is the main subject of this paper. We've realized a system for segmentation and automatic detection of sentence type based on both prosodic, in Berber language, a language where all studies until now are still preliminary. To this end, we developed a corpus made of 720 utterances that were extracted from 6 Berber spoken lectures. Prosodic features are, then, extracted from each sentence. These features are used as input to two different classifiers to classify each sentence into either a question or affirmative sentence. We classified questions with an accuracy of 93%. A feature-specific analysis further reveals that energy and fundamental frequency (F0) features are mainly responsible for discriminating between question and affirmative sentences.
The cardiac pacemaker-specific channel Hcn4 is a direct transcriptional target of MEF2.

AIMS Hcn4, which encodes the hyperpolarization-activated, cyclic nucleotide-sensitive channel (I(h)), is a well-established marker of the cardiac sino-atrial node. We aimed to identify cis-elements in the genomic locus of the Hcn4 gene that regulate the transcription of Hcn4. METHODS AND RESULTS We screened evolutionarily conserved non-coding sequences (CNSs) that are often involved in the regulation of gene expression. The VISTA Enhancer Browser identified 16 regions, termed CNS 1-16, within the Hcn4 locus. Using the luciferase reporter assay in primary neonatal rat cardiomyocytes, we found that CNS13 conferred a prominent enhancer activity (more than 30-fold) on the Hcn4 promoter. Subsequent mutation analysis revealed that the Hcn4 enhancer function was dependent on myocyte enhancer factor-2 (MEF2) and activator protein-1 (AP1) binding sequences located in CNS13. Electrophoretic mobility shift assay and chromatin immunoprecipitation confirmed that MEF2 and AP1 proteins bound CNS13. Furthermore, overexpression of a dominant negative MEF2 mutant inhibited the enhancer activity of CNS13, decreased Hcn4 mRNA expression and also decreased the amplitude of I(h) current in myocytes isolated from the inflow tract of embryonic heart. CONCLUSION These results suggest that the novel enhancer CNS13 and MEF2 may play a critical role in the transcription of Hcn4 in the heart.
Register allocation over the program dependence graph

This paper describes RAP, a Register Allocator that allocates registers over the Program Dependence Graph (PDG) representation of a program in a hierarchical manner. The PDG program representation has been used successfully for scalar optimizations, the detection and improvement of parallelism for vector machines, multiple processor machines, and machines that exhibit instruction level parallelism, as well as debugging, the integration of different versions of a program, and translation of imperative programs for data flow machines. By basing register allocation on the PDG, the register allocation phase may be more easily integrated and intertwined with other optimization analyses and transformations. In addition, the advantages of a hierarchical approach to global register allocation can be attained without constructing an additional structure used solely for register allocation. Our experimental results have shown that on average, code allocated registers via RAP executed 2.7% faster than code allocated registers via a standard global register allocator.
Surgical Efficiencies and Quality in the Performance of Voluntary Medical Male Circumcision (VMMC) Procedures in Kenya, South Africa, Tanzania, and Zimbabwe

Introduction This analysis explores the association between elements of surgical efficiency in voluntary medical male circumcision (VMMC), quality of surgical technique, and the amount of time required to conduct VMMC procedures in actual field settings. Efficiency outcomes are defined in terms of the primary provider’s time with the client (PPTC) and total elapsed operating time (TEOT). Methods Two serial cross-sectional surveys of VMMC sites were conducted in Kenya, Republic of South Africa, Tanzania and Zimbabwe in 2011 and 2012. Trained clinicians observed quality of surgical technique and timed 9 steps in the VMMC procedure. Four elements of efficiency (task-shifting, task-sharing [of suturing], rotation among multiple surgical beds, and use of electrocautery) and quality of surgical technique were assessed as explanatory variables. Mann Whitney and Kruskal Wallis tests were used in the bivariate analysis and linear regression models for the multivariate analyses to test the relationship between these five explanatory variables and two outcomes: PPTC and TEOT. The VMMC procedure TEOT and PPTC averaged 23–25 minutes and 6–15 minutes, respectively, across the four countries and two years. The data showed time savings from task-sharing in suturing and use of electrocautery in South Africa and Zimbabwe (where task-shifting is not authorized). After adjusting for confounders, results demonstrated that having a secondary provider complete suturing and use of electrocautery reduced PPTC. Factors related to TEOT varied by country and year, but task-sharing of suturing and/or electrocautery were significant in two countries. Quality of surgical technique was not significantly related to PPTC or TEOT, except for South Africa in 2012 where higher quality was associated with lower TEOT. Conclusions SYMMACS data confirm the efficiency benefits of task-sharing of suturing and use of electrocautery for decreasing TEOT. Reduced TEOT and PPTC in high volume setting did not result in decreased quality of surgical care.
A planar stable walking model based on ankle actuation and the virtual pendulum concept

In this paper, we propose a novel planar biped model which achieves asymptotically stable walking, based on ankle actuation and the virtual pendulum concept. Simple models for walking have provided useful insights in understanding fundamental principles of human locomotion as well as developing controllers for biped robots. Existing simplest walking models include a point mass with either rigid legs or compliant legs. Both models are able to describe different gaits such as walking and running, but are not able to address posture stabilization, which is another important issue in bipedalism. Recently, the virtual pendulum (VP) concept was proposed as an intuitive posture stabilization strategy and successfully demonstrated on the compliant leg scheme. However, the model does not address inherent peripheral mechanics of walking, i.e., ankle actuation and collisional energy loss from foot-ground interaction. The model proposed in this paper consists of a rigid trunk, rigid legs and ankle actuation. The energy dissipation due to collision and compensation by ankle actuation play an essential role for asymptotically stable walking, while the trunk posture is stabilized based on the VP concept. Nonlinear dynamic simulation verifies that the model constructs a stable limit cycle with a small angular oscillation of trunk.
Pre-Clustering of the B Cell Antigen Receptor Demonstrated by Mathematically Extended Electron Microscopy

The B cell antigen receptor (BCR) plays a crucial role in adaptive immunity, since antigen-induced signaling by the BCR leads to the activation of the B cell and production of antibodies during an immune response. However, the spatial nano-scale organization of the BCR on the cell surface prior to antigen encounter is still controversial. Here, we fixed murine B cells, stained the BCRs on the cell surface with immuno-gold and visualized the distribution of the gold particles by transmission electron microscopy. Approximately 30% of the gold particles were clustered. However the low staining efficiency of 15% precluded a quantitative conclusion concerning the oligomerization state of the BCRs. To overcome this limitation, we used Monte-Carlo simulations to include or to exclude possible distributions of the BCRs. Our combined experimental-modeling approach assuming the lowest number of different BCR sizes to explain the observed gold distribution suggests that 40% of the surface IgD-BCR was present in dimers and 60% formed large laminar clusters of about 18 receptors. In contrast, a transmembrane mutant of the mIgD molecule only formed IgD-BCR dimers. Our approach complements high resolution fluorescence imaging and clearly demonstrates the existence of pre-formed BCR clusters on resting B cells, questioning the classical cross-linking model of BCR activation.
The effects of organizational factors on green new product success: Evidence from high‐tech industries in Taiwan

Purpose – This study seeks to identify the factors influencing the performance of green new product development. Additionally, an examination of the relationship between green performance and financial performance is carried out.Design/methodology/approach – The study employed survey instrument data collected from 181 companies in hi‐tech industries including electrical, electronics, and information industries of Taiwan. Exploratory factor analysis and multiple regressions were used for hypothesis testing.Findings – Corporate environmental commitment, environmental benchmarking, R&D strength, and cross‐functional integration significantly positively influenced financial performance. Additionally, green product innovation performance has a positive effect on financial performance.Research limitations/implications – A longitudinal research design is necessary to validate these claims of causality. Furthermore, since respondents provided data on both the independent and dependent variables, there is the poss.