Miracle-dz/UniFAR-FTUs huggingface dataset:
Formal Verification of Programs and Their Transformations

Formal verification is an act of using formal methods to check the correctness of intended programs. The verification is done by providing a formal proof on an abstract mathematical model of the program, with respect to a certain formal specification or property. We present three case studies on using formal methods to verify programs and their transformations: (1) we use term rewriting and theorem proving to construct and validate a compiler from logic specifications to ARM assembly code; the equivalence of a source specification and the generated assembly code is proven mechanically with respect to the formal semantics; (2) we model, in an \executable" declarative language TLA+, the Message Passing Interface (MPI) 2.0 library as well as C programs using MPI calls for parallel computations; and use explicit model checking to check the specifications and programs; and (3) we model CUDA kernel programs as symbolic logical formulas, and use constraint solving to automatically reason about these Graphics Processing Unit (GPU) kernels. We have built a couple of unique verification tools to check intrinsic properties (e.g. race freedom for concurrent programs and translation correctness for compilers) and user-defined properties (e.g. functional correctness). Specifically, the presented compiler is the first trusted compiler translating logic specifications embedded in a theorem prover to low-level code; the MPI specification is the first attempt to provide executable semantics for a comprehensive set of message passing Application Programming Interfaces (APIs); and the CUDA verifier is the only existing formal symbolic checker for GPU kernel programs.
Central effects of endothelin and its antagonists on sympathetic and cardiovascular regulation in SHR-SP.

Intracerebroventricular injections of endothelin-1 (ET-1) are reported to cause dose-related increases in sympathetic nerve activity and blood pressure in anesthetized normotensive rats. These studies were performed to determine the following: which endothelin receptor, A or B, is involved in mediating sympathetic and cardiovascular effects of ET-1 injected centrally; whether central endothelin tonically participates in blood pressure regulation in normotensive rats; and whether the altered endothelin system in the central nervous system contributes to blood pressure elevation in hypertensive rats. ET-1, ET-A antagonist (BQ-123), or ET-B antagonist (RES-701-1) was injected into the lateral cerebral ventricle (i.c.v.) of urethane-anesthetized normotensive Wistar and Wistar-Kyoto (WKY) rats, spontaneously hypertensive rats (SHRs), and stroke-prone SHRs (SHR-SPs). In Wistar rats, i.c. v. injections of ET-1 (1, 5, 10 pmol) consistently increased sympathetic nerve activity, thereby elevating blood pressure in a dose-related manner. The pressor responses induced by i.c. v. ET-1 were abolished after intravenous pretreatment with phentolamine. Neither ET-A nor ET-B antagonist, when injected centrally, altered basal levels of sympathetic nerve activity, heart rate, or blood pressure in Wistar rats. However, sympathetic activation and pressor responses induced by i.c. v. injection of endothelin were completely abolished after i.c. v. pretreatment with ET-A antagonist but were unaffected after pretreatment with ET-B antagonist. Although i.c. v. injections of ET-1 increased sympathetic nerve activity and blood pressure in WKY rats, SHRs, and SHR-SPs, the magnitudes of these responses did not differ among these three groups. In contrast, i.c. v. injections of ET-A antagonist decreased sympathetic nerve activity, blood pressure, and heart rate only in SHR-SPs, but not in WKY rats and SHRs. In addition, the depressor effects of i.c. v. ET-A antagonist in SHR-SPs were ascertained while these rats were awake. In summary, i.c. v. injections of ET-1 increased sympathetic nerve activity and blood pressure via ET-A receptors but not via ET-B receptors. Central ET might tonically activate sympathetic nerve activity to thereby contribute to blood pressure elevation in SHR-SPs, but not in WKY rats and SHRs.
Methods for Binary Multidimensional Scaling

Multidimensional scaling (MDS) is the process of transforming a set of points in a high-dimensional space to a lower-dimensional one while preserving the relative distances between pairs of points. Although effective methods have been developed for solving a variety of MDS problems, they mainly depend on the vectors in the lower-dimensional space having real-valued components. For some applications, the training of neural networks in particular, it is preferable or necessary to obtain vectors in a discrete, binary space. Unfortunately, MDS into a low-dimensional discrete space appears to be a significantly harder problem than MDS into a continuous space. This article introduces and analyzes several methods for performing approximately optimized binary MDS.
Approaches to Integrating Smart Cards with SSH

The Secure Shell (SSH) tool has greatly improved the security of many networks by providing channel security. This tool is widely used by network and system administrators for remote privileged access to servers and other network devices. It is also used by travellers to conferences and for access to home networks from the network of a customer. In effect it has been a good security replacement for telnet which transfers all information in plaintext. This paper analyses some of the remaining weaknesses of systems even if SSH is used for remote privileged access. It then proposes to use smart cards to address some of the security issues associated with the client side of the connection. A number of the proposals are implemented at this time. A project objective is to publicly release the enhancements to SSH. Work on this paper was performed while employed by Queensland University of Technology. Approaches to Integrating Smart Cards with
The effect of user and channel interferences on QoS routing in Cognitive Radio Ad-Hoc Network

Cognitive Radio Ad-Hoc Network (CRAHN) is an emerging class of mobile ad hoc networks that provides each network node with a list of available channels. It is expected that the traditional routing approach will not work well in CRAHN, by which its performance may be determined by user and channel interferences, as well as by frequent topology changes. The result is varying connectivity conditions being experienced by the mobile nodes. Therefore, to achieve a realistic cognitive routing in CRAHN, the routing protocol and its routing metrics shall be chosen to adapt to propagation and channel conditions. Typically, the aim of any routing protocol is to provide QoS that could be measured by some performance parameters such as average delay and packet delivery ratio. The focus of this work is to justify the effect of user and channel interferences on QoS routing function in CRAHN. Hence, if this justification can be explained, the routing operating conditions can be controlled and the achievement for QoS routing can be more objectively obtained.
EPILEPSY SURGERY AND ELECTRONIC DEVICES

Epilepsy is a chronic disorder characterized by recurrent and unprovoked seizures. The lifetime risk of developing epilepsy is 4%. Approximately 90% of the incident cases in adults have partial epilepsy. The initial response to medication is of prognostic importance. Patients with symptomatic neurologic disease, foreign-tissue lesion, or developmental delay are less likely to be rendered seizure free. The goal of treatment is to render the individual seizure free. Many patients with partial epilepsy will not attain a seizure remission with antiepileptic drug therapy. Epilepsy surgery is an effective and safe alternative form of therapy for selected patients with intractable partial epilepsy. Electronic stimulation is being considered for patients with partial seizures who are not candidates for a focal cortical resection.
Isolation of a TRAIL Antagonist from the Serum of HIV-infected Patients*

Background: The TRAIL:TRAIL receptor system has been implicated in the pathogenesis of a variety of malignant and infectious disorders, including HIV infection. Results: We show that HIV causes production of a novel TRAIL splice variant, that we call TRAIL-short, which binds TRAIL R2, antagonizes TRAIL signaling, and is present in HIV patient samples. Conclusion: Introduction of TRAIL-short causes resistance to TRAIL, whereas knockdown restores sensitivity. Significance: The identification of TRAIL-short impacts our understanding of TRAIL sensitivity and has implications for the pathogenesis of both infectious and malignant pathogenesis. Virus-host interactions are characterized by the selection of adaptive mechanisms by which to evade pathogenic and defense mechanisms, respectively. In primary T cells infected with HIV, HIV infection up-regulates TNF-related apoptosis inducing ligand (TRAIL) and death-inducing TRAIL receptors, but blockade of TRAIL:TRAIL receptor interaction does not alter HIV-induced cell death. Instead, HIV infection results in a novel splice variant that we call TRAIL-short (TRAIL-s), which antagonizes TRAIL-R2. In HIV patients, plasma TRAIL-s concentration increases with increasing viral load and renders cells resistant to TRAIL-induced death. Knockdown of TRAIL-s abrogates this resistance. We propose that TRAIL-s is a novel adaptive mechanism of apoptosis resistance acquired by HIV-infected cells to avoid their elimination by TRAIL-dependent effector mechanism.
Developmental Expression of HSP60 and HSP10 in the Coilia nasus Testis during Upstream Spawning Migration

Heat shock protein 60 (HSP60) and heat shock protein 10 (HSP10) are important chaperones, which have been proven to have essential roles in mediating the correct folding of nuclear encoded proteins imported to mitochondria. Mitochondria are known as the power house of the cell, with which it produces energy and respires aerobically. In this regard, the obtained HSP60 and HSP10 have typical characteristics of the HSP60/10 family signature. Their mRNA transcripts detected were highest during the developmental phase (in April), while the lowest levels were found in the resting phase (after spawning in late July). Additionally, the strongest immunolabeling positive signals were found in the primary spermatocyte, with lower positive staining in secondary sperm cells, and a weak or absent level in the mature sperm. At the electron microscopic level, immunogold particles were localized in the mitochondrial matrix. Data indicated that HSP10 and HSP60 were inducible and functional in the Coilia nasus testis development and migration process, suggesting their essential roles in this process. The results also indicated that HSP60 may be one indicator of properly working mitochondrial import and refolding in the fish testis. This study also provides an expanded perspective on the role of heat shock protein families in spawning migration biology.
Genetically resistant sheep avoid parasites to a greater extent than do susceptible sheep

Livestock breeding programmes have created resistant (R) and susceptible (S) sheep that differ in their ability to control parasites through their immune function but potentially also their grazing behaviour (i.e. parasite avoidance). Using the Perendale genetic lines, we tested the hypothesis that R-sheep avoid parasites more effectively, reducing their parasite exposure/challenge, compared with S-sheep. However, in grazing systems, parasite-rich areas are also forage rich, suggesting that parasite avoidance behaviours are associated with nutritional penalties. We first created a naturally heterogeneous sward structure of gaps and tussocks and then used focal behavioural observations to quantify the sward selection of R- and S-sheep. Tussock swards were more nitrogen rich (41%), offered increased forage intake rates (32%) and contained 17 times more parasite larvae than gap swards. All the animals avoided grazing the tussock swards. However, the R-sheep grazed the tussock swards to a lesser degree than the S-sheep. We conclude that selection for genetic resistance has resulted in animals that, despite being well armed to fight parasitism through improved immune function, adopt parasite avoidance strategies with associated nutritional disadvantages. This experiment highlights the role of host behaviour in the control of parasitism and suggests that animals can be bred to avoid disease.
Genome‐wide association study discovered candidate genes of Verticillium wilt resistance in upland cotton (Gossypium hirsutum L.)

Summary Verticillium wilt (VW), caused by infection by Verticillium dahliae, is considered one of the most yield‐limiting diseases in cotton. To examine the genetic architecture of cotton VW resistance, we performed a genome‐wide association study (GWAS) using a panel of 299 accessions and 85 630 single nucleotide polymorphisms (SNPs) detected using the specific‐locus amplified fragment sequencing (SLAF‐seq) approach. Trait–SNP association analysis detected a total of 17 significant SNPs at P < 1.17 × 10–5 (P = 1/85 630, –log10 P = 4.93); the peaks of SNPs associated with VW resistance on A10 were continuous and common in three environments (RDIG2015, RDIF2015 and RDIF2016). Haplotype block structure analysis predicted 22 candidate genes for VW resistance based on A10_99672586 with a minimum P‐value (–log10 P = 6.21). One of these genes (CG02) was near the significant SNP A10_99672586 (0.26 Mb), located in a 372‐kb haplotype block, and its Arabidopsis AT3G25510 homologues contain TIR‐NBS‐LRR domains that may be involved in disease resistance response. Real‐time quantitative PCR and virus‐induced gene silencing (VIGS) analysis showed that CG02 was specific to up‐regulation in the resistant (R) genotype Zhongzhimian2 (ZZM2) and that silenced plants were more susceptible to V. dahliae. These results indicate that CG02 is likely the candidate gene for resistance against V. dahliae in cotton. The identified locus or gene may serve as a promising target for genetic engineering and selection for improving resistance to VW in cotton.
Outbreak of isoniazid resistant tuberculosis in north London

Background: A description is given of a major outbreak of isoniazid monoresistant tuberculosis (TB) chiefly in north London, including prisons. The earliest case was diagnosed in 1995 with most cases appearing after 1999. Methods: Confirmation of a local cluster of cases was confirmed by restriction fragment length polymorphism (RFLP IS6110) typing or “rapid epidemiological typing” (RAPET). Further cases were found by retrospective analysis of existing databases, prospective screening of new isolates, and targeted epidemiological case detection including questionnaire analysis. Results: By the end of 2001, 70 confirmed cases in London had been linked with a further 13 clinical cases in contacts and nine epidemiologically linked cases outside London. The epidemic curve suggests that the peak of the outbreak has not yet been reached. Cases in the outbreak largely belong to a social group of young adults of mixed ethnic backgrounds including several individuals from professional/business backgrounds. Compared with other cases of TB reported to the enhanced surveillance scheme in London during 1999–2001, the cases are more likely to be of white (26/70 (37%) v 1308/7666 (17%)) or black Caribbean ethnicity (17/70 (24%) v 312/7666 (4%)), born in the UK (41/70 (59%) v 1335/7666 (17%)), and male (52/70 (74%) v 4195/7666 (55%)). Drug misuse and/or prison detention are factors common to many cases. Conclusions: The investigation of the outbreak revealed significant problems on an individual patient and population based level including difficulties with contact tracing, compliance, and the risk of developing multidrug resistance. This incident has demonstrated the value of molecular strain typing in investigating an extensive outbreak of TB. This is the first documented outbreak involving a UK prison.
Cloud-based Connected Component Algorithm

The connected component of an undirected graph plays an important part in graph theory. It is straightforward to compute the connected components of a graph in linear time using either breadth-first search or depth-first search. However when confronted with large scale data, both of the two algorithms are hard to execute. In this paper, we introduce a recently proposed community detection technique by label propagation discussed in [1]. And based on the label propagation algorithm (LPA), we propose a method to compute the connected components of an undirected graph. The method is on top of cluster system with the help of MapReduce, and implemented to fully utilize MapReduce execution mechanism, namely the “map-reduce” process. Moreover, considering how our algorithm can be applied in further “cloud” service, we employ several large scale datasets to demonstrate the efficiency and scalability of our solutions.
Survivin, Ki-67 and tumor grade as predictors of response to docetaxel-based neoadjuvant chemotherapy in locally advanced breast cancer

The response rates to neoadjuvant chemotherapy (NAC) in patients with locally advanced breast cancer (LABC) may vary and the risks may outweigh the benefits in poorly selected patients. This study investigated whether survivin expression, high-level Ki-67 expression, estrogen-receptor (ER) tumor status and high tumor grade are able to predict response to docetaxel-based NAC in LABC patients, in order to perform breast-conserving surgery. In this study, 68 patients (IIb-IIIb) completed 4–6 cycles of TAC (75 mg/m2 docetaxel, 60 mg/m2 pirarubicin and 500 mg/m2 cyclophosphamide, administered every 3 weeks). Tumor samples were obtained prior to chemotherapy. The response to chemotherapy was quantified clinically and pathologically and the histological and molecular tumor characteristics were determined. Association with response was assessed for all the parameters and the patients underwent breast-conserving surgery or radical mastectomy accordingly. A clinical complete response was observed in 21 (31%) and a partial response in 37 (54%) of the 68 patients. Thus, the overall clinical response rate (ORR) was 85%. A pathological complete response (pCR) was observed in 14 (20%) of the 68 patients and 37 patients (54%) underwent breast-conserving surgery. In the univariate analysis, survivin expression, high-level Ki-67 expression and high tumor grade (grade III) were significantly associated with ORR (P=0.007, 0.024 and 0.047, respectively). Survivin expression and high-level Ki-67 expression were significantly associated with pCR (P=0.029 and 0.048, respectively). In the multivariate analysis, survivin expression (P=0.030) and tumor grade (P=0.036), but not high-level Ki-67 and ER expression, were significantly associated with ORR and none of these factors was significantly associated with pCR. In conclusion, expression of survivin and high tumor grade were of predictive value for ORR to docetaxel-based NAC in LABC patients, leading to more patients successfully undergoing breast conserving-surgery. Immunohistochemistry of survivin and the Elston and Ellis criteria of tumor grade may provide a widely applicable, cost-effective method of patient selection for NAC.
Acquisition of nicotine discrimination and discriminative stimulus effects of nicotine in rats chronically exposed to caffeine.

Caffeine and nicotine are the main psychoactive ingredients of coffee and tobacco, with a high frequency of concurrent use in humans. This study examined the effects of chronic caffeine exposure on 1) rates of acquisition of a nicotine discrimination (0.1 or 0.4 mg/kg, s.c., training doses) and 2) the pharmacological characteristics of the established nicotine discrimination in male Sprague-Dawley rats. Once rats learned to lever-press reliably under a fixed ratio of 10 schedule for food pellets, they were randomly divided into two groups; 12 animals were maintained continuously on caffeine added to the drinking water (3 mg/ml) and another 12 control rats continued to drink tap water. In each group of water- and caffeine-drinking rats, there were six rats trained to discriminate 0.1 mg/kg of nicotine from saline and six rats trained to discriminate 0.4 mg/kg of nicotine from saline. Regardless of the training dose of nicotine, both water- and caffeine-drinking groups required a comparable number of training sessions to attain reliable stimulus control, although there was a trend for a slower acquisition in the caffeine-drinking group trained with 0.1 mg/kg of nicotine. Tests for generalization to different doses of nicotine revealed no significant differences in potency of nicotine between water- and caffeine-drinking groups. The nicotinic-receptor antagonist mecamylamine blocked the discriminative effects of 0.1 and 0.4 mg/kg nicotine with comparable potency and efficacy in water- and caffeine-drinking groups. There was a dose-related generalization to both the 0.1 and 0.4 mg/kg nicotine cue (maximum average of 51-83%) in water-drinking rats after i.p. treatment with d-amphetamine, cocaine, the selective dopamine uptake inhibitor GBR-12909, apomorphine, and the selective dopamine D1 receptor agonist SKF-82958, but not in caffeine-drinking rats (0-22%). There was no generalization to the nicotine cues after i.p. treatment with caffeine or the selective D2 (NPA) and D3 (PD 128,907) dopamine-receptor agonists in water- and caffeine-drinking rats. The dopamine-release inhibitor CGS 10746B reduced the discriminative effects of 0.4 mg/kg nicotine in water-drinking rats, but not in caffeine-drinking rats. There was no evidence of development of tolerance or sensitization to nicotine's effects throughout the study. In conclusion, chronic caffeine exposure (average, 135 mg/kg/day) did not affect the rate of acquisition of the nicotine discrimination, but it did reduce the dopaminergic component of the nicotine-discriminative cue. The reduction of the dopaminergic component of the nicotine cue was permanent, as this effect was still evident after the caffeine solution was replaced with water in caffeine-drinking rats. That nicotine could reliably serve as a discriminative stimulus in the absence of the dopaminergic component of its discriminative cue may differentiate nicotine from "classical dopaminergic" drugs of abuse such as cocaine and amphetamine.
Apparition: Crowdsourced User Interfaces that Come to Life as You Sketch Them

Prototyping allows designers to quickly iterate and gather feedback, but the time it takes to create even a Wizard-of-Oz prototype reduces the utility of the process. In this paper, we introduce crowdsourcing techniques and tools for prototyping interactive systems in the time it takes to describe the idea. Our Apparition system uses paid microtask crowds to make even hard-to-automate functions work immediately, allowing more fluid prototyping of interfaces that contain interactive elements and complex behaviors. As users sketch their interface and describe it aloud in natural language, crowd workers and sketch recognition algorithms translate the input into user interface elements, add animations, and provide Wizard-of-Oz functionality. We discuss how design teams can use our approach to reflect on prototypes or begin user studies within seconds, and how, over time, Apparition prototypes can become fully-implemented versions of the systems they simulate. Powering Apparition is the first self-coordinated, real-time crowdsourcing infrastructure. We anchor this infrastructure on a new, lightweight write-locking mechanism that workers can use to signal their intentions to each other.