Miracle-dz/UniFAR-FTUs huggingface dataset:
Building Reliable Software for Persistent Memory

Author(s): Zhang, Lu | Advisor(s): Swanson, Steven | Abstract: Persistent memory (PMEM) technologies preserve data across power cycles and provide performance comparable to DRAM. In emerging computer systems, PMEM will operate on the main memory bus, becoming byte-addressable and cache-coherent. One key feature enabled by persistent memory is to allow software directly accessing durable data using the CPU’s load/store instructions, even from the user-space.However, building reliable software for persistent memory faces new challenges from two aspects: crash consistency and fault tolerance. Maintaining crash consistency requires the ability to recover data integrity in the event of system crashes. Using load/store instructions to access durable data introduces a new programming paradigm, that is prone to new types of programming errors. Fault tolerance involves detecting and recovering from persistent memory errors, including memory media errors and scribbles from software bugs. With direct access, file systems and user-space applications have to explicitly manage these errors, instead of relying on convenient functions from lower I/O stacks.We identify unique challenges in improving reliability for PMEM-based software and propose solutions. The thesis first introduces NOVA-Fortis, a fault-tolerant PMEM file system incorporating replication, checksums, and parity for protecting the file system’s metadata and the user’s file data. NOVA-Fortis is both fast and resilient in the face of corruption due to media errors and software bugs.NOVA-Fortis only protects file data via the read() and write() system calls. When an application memory-maps a PMEM file, NOVA-Fortis has to disable file data protection because mmap() leaves the file system unaware of updates made to the file. For protecting memory-mapped PMEM data, we present Pangolin, a fault-tolerant persistent object library to protect an application’s objects from persistent memory errors.Writing programs to ensure crash consistency in PMEM remains challenging. Recovery bugs arise as a new type of programming error, preventing a post-crash PMEM file from recovering to a consistent state. Thus, we design two debugging tools for persistent memory programming: PmemConjurer and PmemSanitizer. PmemConjurer is a static analyzer using symbolic execution to find recovery bugs without running a compiled program. PmemSanitizer contains compiler instrumentation and run-time recovery bug analysis, compensating PmemConjurer with multi-threading support and store reordering tests.
Studies on a CO2-dependent staphylococcus.

A dwarf strain of Staphylococcus aureus was isolated in pure culture from styes on the eyelid of a young woman. Incubation of pus cultured on horse blood agar in 5% CO2 yielded a typical golden staphylococcus, coagulase and catalase positive and penicillin sensitive, but on duplicate plates in air the growth was of tiny white colonies only 0.25 mm. in diameter. These were penicillin-sensitive Gram-positive cocci, but the catalase and coagulase tests were negative.
IMPLEMENTATION OF SCHOOL CULTURE PROGRAM IN CHARACTER EDUCATION STRENGTHENING

Schools have an important role in providing basic concepts to shape student personality through character education. Therefore, schools must design and manage activities that internalize character education to improve quality human resources. Strengthening Character Education (KDP) through the application of school culture is one of the efforts to develop character building in schools. The application of school culture programs in each educational institution has its own uniqueness. Among the schools that have their own unique character in the Character Building Strengthening (PPK) program are the Integrated Islamic Elementary School (SDIT) Ummul Quro Bogor. Among the characters developed by SDIT Ummul Quro are called 8 My habits, namely: 1) polite satun, 2) clean and neat, 3) prayer with awareness, 4) birrul waalidain (good to both parents), 5) discipline, 6) honest , 7) the spirit of recitations and memorization of the Koran, and 8) learners. This research was conducted aiming to analyze the implementation of school culture programs in strengthening the 8 Habku character as the development of KDP SDIT Ummul Quro. The method used is descriptive qualitative. Data obtained by observation, interview, and documentation study. The results showed that the implementation of the school culture program made a good contribution to the development of KDP students at SDIT Ummul Quro. The results of this study imply that the school culture program needs to be implemented as part of a way to shape student character.
Aspects diagnostiques et thérapeutiques du modèle d'ischémie - reperfusion mésentérique

Introduction: La lesion d'ischemie - reperfusion (I/R) intestinale est associee a une mortalite elevee.Le role de la transmigration des neutrophiles est probablement essentiel dans le dysfonctionnement de la barriere induit par la lesion I/R et la necrose subsequente. Le but de notre etude etait d'evaluer, au niveau pre-clinique, la valeur therapeutique potentielle du peptide P8RI (un agoniste de CD31) dans la lesion I/R de l'intestine grele.Methodes: I/R intestinale a ete induite chez des rats Wistar par clampage de l'artere mesenterique superieure (AMS) pendant 30 min suivi par 4 h de reperfusion. Trois groupes de rats ont ete compares:P8RI (n = 20, I/R et P8RI 2,5 mg/kg/h de reperfusion), I/R temoins positifs (n = 21, I/R et infusion de serum physiologique) et temoins (n = 14, dissection de l'AMS sans clampage et infusion de serum physiologique). La matrix metallopeptidase 9 (MMP-9) dans la plasma, le liquide peritoneal et l'intestin; la MPO intestinale, l'ADN libre plasmatique, les taux d'hemoglobine intraluminale e tl'epaisseur epitheliale ont ete evalues comme marqueurs intermediaires de la lesion intestinale. La detection du materiel genetique d'E.coli par PCR quantitative dans le sang a ete egalement realisee chez les temoins positifs et chez les rats traites par P8RI pendant la periode de reperfusion. Le CD31clive dans le plasma a ete mesure par une methode d'ELISA maison. Resultats: La grade histologique de l'intestin grele chez les animaux traites par P8RI est superieur acelui des temoins positifs d'I/R (p < 0,05). P8RI protege l'intestin grele contre la destruction epitheliale induite par lesion I/R (p < 0,01). Il y a une correlation negative significative entre l'abrasion epitheliale et le score de Chiu de classement histologique de la lesion I/R mesenterique (r = -0,7245, p < 0.001). P8RI protege l'intestin grele de la MPO in situ, de la liberation de la MMP-9 (p < 0,05) et des complications hemorragiques digestives causees par lesion I/R (p < 0,01). Les taux plasmatiques et peritoneaux accrus de MMP-9, induits par I/R, sont significativement reduits par P8RI (p < 0,05 et p <0,01, respectivement). L'ADN d'E.coli circulant est significativement plus eleve chez les rats de temoins positifs que dans le groupe P8RI (p < 0,05). L'ADN libre plasmatique pendant la reperfusion chez les rats de temoins positifs augmente significativement plus que celle des rats du groupe P8RI (p< 0,05). P8RI n'a aucun effet sur le compte neutrophilaire sanguin, mais induit une diminution significative de CD31 clive dans le plasma pendant l'I/R mesenterique (p < 0,01). Les correlations entre l'abrasion epitheliale et l'ADN libre, MMP-9, CD31 clive plasmatiques, les taux de MMP-9 et MPO intestinale suggerent que le mecanisme protecteur de P8RI implique l'inhibition de l'activation neutrophilaire, y compris le clivage de CD31. Conclusions: Cette etude suggere que le traitement par le peptide P8RI, un agoniste de CD31, reduit de la facon preventive, la lesion I/R de l'intestin grele chez les rats.
Optimal Runtime Algorithm to Improve Fault Tolerance of Bus-Based Reconfigurable Designs

This article presents an approach to providing fault tolerance to permanent effects in the substrate of dynamic, partially reconfigurable field-programmable gate arrays (FPGAs). Our proposal consists of modifying FPGA configuration at runtime to avoid permanently damaged regions of the FPGA. It demands that the circuit design fulfills several requirements regarding the functionality and interfaces of its reconfigurable modules, the structure of the communications, the inclusion of specialized modules to handle and optimize circuit reconfiguration at runtime, and the organization of the reconfigurable partitions. We evaluate two methods to select the new target partition for modules in faulty partitions and design their hardware as intellectual property modules. We evaluate the performance and scalability of this approach using a trapezoidal shaper, a filter used to detect high-energy particles in radiation experiments, and we carry out the experiments with a variable number of modules and reconfigurable partitions using the two selection algorithms. The proposal is compared with nonfault-tolerant and triple modular redundancy approaches, and it remains functional with up to $12\times $ more injected faults than those.
Drag-induced directionality switching of kinesin-5 Cin8 revealed by cluster-motility analysis

Directionality switching of the mitotic kinesin-5 Cin8 motor is caused by an asymmetric response of its active movement to drag. Directed active motion of motor proteins is a vital process in virtually all eukaryotic cells. Nearly a decade ago, the discovery of directionality switching of mitotic kinesin-5 motors challenged the long-standing paradigm that individual kinesin motors are characterized by an intrinsic directionality. The underlying mechanism, however, remains unexplained. Here, we studied clustering-induced directionality switching of the bidirectional kinesin-5 Cin8. Based on the characterization of single-molecule and cluster motility, we developed a model that predicts that directionality switching of Cin8 is caused by an asymmetric response of its active motion to opposing forces, referred to as drag. The model shows excellent quantitative agreement with experimental data obtained under high and low ionic strength conditions. Our analysis identifies a robust and general mechanism that explains why bidirectional motor proteins reverse direction in response to seemingly unrelated experimental factors including changes in motor density and molecular crowding, and in multimotor motility assays.
Terrestrial animal health code 2015. Volume 2: recommendations applicable to OIE listed diseases and other diseases of importance to international trade.

The value of the Terrestrial Code is twofold: firstly, the sanitary measures recommended are the result of consensus among the Veterinary Authorities of OIE Members, and secondly, it constitutes a reference for terrestrial animals within the WTO SPS Agreement as an international standard for animal health and zoonoses, as well as a key standard for the prevention and control of animal diseases. The standards in the Terrestrial Code are based on the most recent scientific and technical information and have been formally adopted by the World Assembly of OIE Delegates. Correctly applied, they protect animal health and welfare and veterinary public health during production and trade in animals and animal products while avoiding unjustified sanitary barriers to trade. Given the formal recognition of OIE standards, recommendations and guidelines in the WTO Agreement on the Application of Sanitary and Phytosanitary Measures, the Terrestrial Code is also a key part of the WTO legal framework for international trade. Volume II contains disease-specific standards for OIE listed diseases including foot and mouth disease; infection with avian influenza viruses; bovine spongiform encephalopathy; infection with African horse sickness virus; peste des petit ruminants and classical swine fever.
Analysis of the process of loosening the rocks with different strength properties using the undercutting bolts

The process and the test results of the solid rock loosening by use of the fixed undercutting bolt are described. The tests were carried out within the RODEST project, OPUS 10 competition No. 2015/19/B/ST10/02817, financed by the National Science Centre, where a series of numerical modelling as well as laboratory and in-situ tests were planned. The test stand equipment as well as methodology for conducting the in-situ tests are presented. The tests were conducted in four mines. In each mine tens of solid rock loosening tests were conducted, during which the process parameters were recorded. Additionally, the loosened area outline in each successful test was recreated using 3D scanner. Data collected during in-situ tests as well as strength properties of the tested rocks enabled analysing the loosening process (forces, ranges) in relation to the rock type.
Nuclear Magnetic Resonance Characterization of Petrophysical Properties in Tight Sandstone Reservoirs

Permeability and bound water saturation (Swb) are key parameters reflecting the petrophysical properties of porous rocks. Nuclear magnetic resonance (NMR) has proved to be effective in investigating the properties of porous media. However, estimating Swb and the permeability in tight sandstone reservoirs based on conventional NMR methods, which requires the inversion of NMR echo data to obtain the transverse relaxation time (T2) distribution, proves to be a challenging task. In this study, a method is proposed to estimate Swb and the permeability in tight sandstone reservoirs based on the direct analysis of NMR echo data, thus avoiding the inversion process. A total of 20 tight sandstone samples from the Ordos Basin in China was taken for laboratory NMR measurements. The kernel function of the echo data was used to characterize the ratio distribution of bound water volume to pore volume for different pore sizes. Following this, an echo data calibration method was applied to estimate Swb without the inversion of the T2 distribution, and the window method was used to reduce the impact of noise in the echo data. Furthermore, models for estimating permeability were proposed based on the determined windows of the NMR echo data in the Swb estimation. The reliability of the proposed method for estimating Swb and permeability was verified by comparing the estimated and experimental results. Our study provides an efficient method for the estimation of petrophysical parameters in porous rocks based on the direct analysis of NMR echo data.
BIOCHEMICAL AND HISTOPATHOLOGICAL CHANGES OF TRADITIONAL SIDDHA FORMULATION ON CCL4 INDUCED LIVER FIBROSIS IN RATS

ABSTRACT Objective: The main objective of this study is to evaluate therapeutic activity of traditional siddha formulation on CCl4 induced liver fibrosis in rats. Methods: Plant materials collected, shade dried, mixed equal proportion. This mixture was used for extract or kasayam preparation. Twenty four male Wistar albino rats were randomly divided into four groups of six rats each. The normal control group was allowed free access to food and water. Drug control group was allowed to daily intragastric administration of traditional siddha formulation 400mg per kg b.wt per day. Liver damage was performed in the remaining two groups with an i.p.injection of a 1.0 mL/kg b.wt CCl 4 and olive oil (2:3 v/v) mixture, twice weekly for 8 weeks. All rats, with the exception of the injury model group, were intragastrically administered traditional siddha formulation ( TSF ) dosage 400 mg/ kg b.wt /day from 5 th week to end of experiment of CCl4 intoxicated rats. The serum levels of hepatic markers and hydroxyproline (Hyp) in the rat livers were measured. Histopathological changes in the liver were assessed for each group using H&E staining and Masson Trichrome examination. Results: Traditional siddha formulation significantly reverse the liver function in CCl4 intoxicated rats correlate with both biochemical and histopathological changes Conclusion: Traditional siddha formulation a promising drug for treating liver fibrosis. Keywords: Traditional siddha formulation, Liver fibrosis, CCl4 and Vaithiyars
In What Measure Is Public Finance Sustainability Threatened by Illicit Tobacco Trade: The Case of Western Balkan Countries

The aim of this paper is to gain new knowledge about illicit tobacco trade in Western Balkan countries and its effects on public finance sustainability. It includes an estimation of the volume of illicit tobacco trade, identifying and quantifying the key factors that cause illegal tobacco trade, the effects of illegal tobacco trade on public finance sustainability, and the effects on the intensity of total tobacco trade. An empirical analysis was conducted using the data collected by field research on consumer preferences in tobacco products in Western Balkan countries (Bosnia and Herzegovina, Croatia, Kosovo, Macedonia, Montenegro, Serbia, and Slovenia). The reference research period is the year 2018. The results obtained show a high variability of volume of illicit tobacco trade in Western Balkan countries. While more than 20% of tobacco products in Montenegro and Bosnia and Herzegovina are bought on the gray market, a share of illicit tobacco trade lower than 5% is found in Slovenia and Macedonia. Underdeveloped institutional framework fighting against illicit trade and weak rule of law, coupled with the heavy taxation of tobacco products, are the key factors behind a higher intensity of illicit trade in comparison to more developed European Union (EU) economies. Illicit tobacco trade negatively affects the stability of public finance of Western Balkan economies and reduces the level of public service. It is especially important for the health system combating the negative consequences of smoking. Regular and illicit tobacco trade amongst Western Balkan countries is found to flow in opposite directions.
Improved Iterative Learning Control Strategy for Surface-Mounted Permanent Magnet Synchronous Motor Drives

In this article, an improved iterative learning control (ILC), which significantly enhances the speed tracking performance in the transient and steady state for a surface-mounted permanent magnet synchronous motor (SPMSM) drive, is proposed. The proposed ILC encapsulates two control terms: the feedback linearization control terms force the speed error to approach zero, and the iterative learning control terms (ILCTs) improve the performance of the control inputs based on the stored data such as previous speed error and previous control input. Unlike the conventional feedback linearization control (FLC), the proposed ILC does not require the exact information of the SPMSM parameters, significantly rejects the periodic and nonperiodic disturbances, and efficiently provides an enhanced speed tracking performance owing to the included ILCTs. Besides, its stability is proven by showing that the speed tracking error asymptotically goes to zero. In comparative studies, the proposed method offers the better transient performance (e.g., faster transient response and smaller overshoot) and steady-state performance (i.e., smaller steady-state error) than the conventional FLC under load and speed step changes. To prove the practicability of the proposed scheme, the proposed ILC is simulated and implemented on a MATLAB/Simulink software and a prototype SPMSM test-bed using TI TMS320F28335 digital signal processor, respectively.
Signaling during Mechanical Strain Injury of the Urinary Bladder: ERK, STAT3 and mTOR Pathways

Bladder obstruction (neurogenic or anatomic) induces strain injury in detrusor smooth muscle cells. Signaling via strain injury in other systems has been highly studied, while in bladder obstruction, it has been quite limited to a small number of pathways. In our study we have examined the effects of strain injury using a combination of in vivo, ex vivo and in vitro models, with the aim of understanding disease pathogenesis in the bladder. Using a combination of literature searches, phospho-protein screens and pathway analysis, we uncovered three pathways activated by mechanical strain, ERK, STAT3 and mTOR, with potential for changing not only the way we understand but also the way we treat obstructive myopathies of the bladder. We found that not only were these pathways activated in response to strain and distension injury of BSMC, but they were also responsible for proliferation and sometimes de-differentiation. Included herein are three chapters, published in 2006 and 2010, on the role of ERK, STAT3 and mTOR pathways in bladder smooth muscle cell proliferation and differentiation, 8 Appendices containing the first pages of other papers and reviews published during the course of my studies.
Molecular Mechanism of the Immunomodulatory Drug Halofuginone

Cellular sensing of amino acid availability has recently emerged as an important mechanism of immunomodulation. Small molecules that manipulate amino acid metabolism serve as powerful tools for studying these poorly characterized signaling pathways. The compound halofuginone, derived from an herb in traditional Chinese medicine, induces a cellular state of proline starvation by inhibiting the prolyl-tRNA synthetase domain of EPRS. The resulting accumulation of uncharged prolyl-tRNA correlated with inhibition of Th17 differentiation and protection against autoimmune disease. Halofuginone invoked the canonical amino acid starvation response (AAR) by increasing phosphorylation of GCN2 and eIF2α to adapt to nutrient stress. However, knockout of GCN2 failed to fully account for the antiinflammatory properties of halofuginone and did not rescue Th17 differentiation, suggesting immunomodulation through non-canonical AAR pathways. Since GCN2-independent AAR pathways are better characterized in yeast than in mammals, we identified and investigated their orthologs. Co-immunoprecipitation studies validated the formation of an orthologous human GCN1/RWDD1/DRG2 complex. Knockdown of the adaptor protein RWDD1 in fibroblast-like synoviocytes reduced the ability of halofuginone to suppress CXCL10 and MMP-13 expression during TNF-α-induced inflammation. A non-canonical AAR pathway involving GCN1, RWDD1, and DRG2 could expand our understanding of how amino acid metabolism regulates immunity and may reveal new drug targets for immunotherapy.
Cigarette Smoking: An Accessory to the Development of Insulin Resistance

Insulin resistance is a condition characterized by decreased sensitivity of a skeletal or adipose cell to insulin, resulting in decreased glucose uptake by the cell. This can lead to hyperinsulinemia and further reduce insulin sensitivity. Insulin resistance is one of the primary factors contributing to metabolic syndrome (MetS), causing elevated glucose and fatty acid concentrations in the blood. Smoking is associated with insulin resistance in a dose-dependent manner. It directly increases the risk for insulin resistance, mainly via hormone activation, and may indirectly cause insulin resistance due to its effects on abdominal obesity. Nicotine may be the factor underlying these potential mechanisms. With the prevalence of prediabetes and diabetes on the rise, and considering the role of smoking and its relationship to insulin resistance, smoking reduction or cessation may be a viable option for those who are at risk or already identified as insulin resistant. Therefore, smoking cessation or reduction would serve as a beneficial component in any diabetes prevention or treatment plan.