Miracle-dz/UniFAR-FTUs huggingface dataset:
Scratchpad Sharing in GPUs

General-Purpose Graphics Processing Unit (GPGPU) applications exploit on-chip scratchpad memory available in the Graphics Processing Units (GPUs) to improve performance. The amount of thread level parallelism (TLP) present in the GPU is limited by the number of resident threads, which in turn depends on the availability of scratchpad memory in its streaming multiprocessor (SM). Since the scratchpad memory is allocated at thread block granularity, part of the memory may remain unutilized. In this article, we propose architectural and compiler optimizations to improve the scratchpad memory utilization. Our approach, called Scratchpad Sharing, addresses scratchpad under-utilization by launching additional thread blocks in each SM. These thread blocks use unutilized scratchpad memory and also share scratchpad memory with other resident blocks. To improve the performance of scratchpad sharing, we propose Owner Warp First (OWF) scheduling that schedules warps from the additional thread blocks effectively. The performance of this approach, however, is limited by the availability of the part of scratchpad memory that is shared among thread blocks. We propose compiler optimizations to improve the availability of shared scratchpad memory. We describe an allocation scheme that helps in allocating scratchpad variables such that shared scratchpad is accessed for short duration. We introduce a new hardware instruction, relssp, that when executed releases the shared scratchpad memory. Finally, we describe an analysis for optimal placement of relssp instructions, such that shared scratchpad memory is released as early as possible, but only after its last use, along every execution path. We implemented the hardware changes required for scratchpad sharing and the relssp instruction using the GPGPU-Sim simulator and implemented the compiler optimizations in Ocelot framework. We evaluated the effectiveness of our approach on 19 kernels from 3 benchmarks suites: CUDA-SDK, GPGPU-Sim, and Rodinia. The kernels that under-utilize scratchpad memory show an average improvement of 19% and maximum improvement of 92.17% in terms of the number of instruction executed per cycle when compared to the baseline approach, without affecting the performance of the kernels that are not limited by scratchpad memory.
Univer sity of Amsterdam Programming Research Group On the Operating Unit Size of Load / Store Architectures

We introduce a strict version of the concept of a load/store instruction set architecture in the setting of Maurer machines. We take the view that transformations on the states of a Maurer machine are achieved by applying threads as considered in thread algebra to the Maurer machine. We study how the transformations on the states of the main memory of a strict load/store instruction set architecture that can be achieved by applying threads depend on the operating unit size, the cardinality of the instruction set, and the maximal number of states of the threads.
Morquio A Syndrome: Identification of Differential Patterns of Molecular Pathway Interactions in Bone Lesions

Mucopolysaccharidosis type IVA (MPS IVA; Morquio A syndrome) is a rare autosomal recessive lysosomal storage disease (LSD) caused by deficiency of a hydrolase enzyme, N-acetylgalactosamine-6-sulfate sulfatase, and characterized clinically by mainly musculoskeletal manifestations. The mechanisms underlying bone involvement in humans are typically explored using invasive techniques such as bone biopsy, which complicates analysis in humans. We compared bone proteomes using DDA and SWATH-MS in wild-type and MPS IVA knockout mice (UNT) to obtain mechanistic information about the disease. Our findings reveal over 1000 dysregulated proteins in knockout mice, including those implicated in oxidative phosphorylation, oxidative stress (reactive oxygen species), DNA damage, and iron transport, and suggest that lactate dehydrogenase may constitute a useful prognostic and follow-up biomarker. Identifying biomarkers that reflect MPS IVA clinical course, severity, and progression have important implications for disease management.
Implementasi Metode Weight Aggregated Sum Product Assesment (Waspas) Dalam Pemilihan Lokasi Cabang Baru Penjualan Bakery

Maraknya penikmat roti (bakery) memberikan peluang bagi perusahaan yang bergerak dalam penjualan bakery untuk mengembangkan usaha mereka. Salah satu cara pengembangan yang dilakukan adalah dengan membuka cabang-cabang penjualan. Pemilihan lokasi sering kali dianggap sebagai hal yang sepele, padahal lokasi usaha sangat menentukan keberlangsungan dari usaha yang dilakukan. Untuk membangun lokasi usaha baru khususnya pembukaan cabang baru tidaklah mudah dikarenakan harus tepat, strategis dan efisien agar usaha tersebut dapat diterima dengan mudah oleh konsumen. Untuk pemilihan lokasi cabang dapat mempertimbangkan beberapa aspek, diantaranya aksesibilitas (kemudahan untuk diakses), visibilitas (kemudahan untuk dilihat), lingkungan sekitar dan persaingan. Penelitian ini mengadopsi metode Weight Aggregated Sum Product Assesment (WASPAS) dalam sistem pendukung keputusan untuk mempermudah proses pemilihan lokasi cabang terbaik berdasarkan penilaian dari aspek-aspek yang telah ditentukan. Metode WASPAS merupakan metode yang dapat mengurangi kesalahan-kesalahan atau mengoptimalkan dalam penaksiran untuk penentuan nilai tertinggi dan terendah.
Anchoring Intrinsically Disordered Proteins to Multiple Targets: Lessons from N-Terminus of the p53 Protein

Anchor residues, which are deeply buried upon binding, play an important role in protein–protein interactions by providing recognition specificity and facilitating the binding kinetics. Up to now, studies on anchor residues have been focused mainly on ordered proteins. In this study, we investigated anchor residues in intrinsically disordered proteins (IDPs) which are flexible in the free state. We identified the anchor residues of the N-terminus of the p53 protein (Glu17–Asn29, abbreviated as p53N) which are involved in binding with two different targets (MDM2 and Taz2), and analyzed their side chain conformations in the unbound states. The anchor residues in the unbound p53N were found to frequently sample conformations similar to those observed in the bound complexes (i.e., Phe19, Trp23, and Leu26 in the p53N-MDM2 complex, and Leu22 in the p53N-Taz2 complex). We argue that the bound-like conformations of the anchor residues in the unbound state are important for controlling the specific interactions between IDPs and their targets. Further, we propose a mechanism to account for the binding promiscuity of IDPs in terms of anchor residues and molecular recognition features (MoRFs).
Marriage and Fertility under Military Occupation: A Study of the West Bank of Palestine

We investigate effects of the Israeli Occupation of the West Bank on rate of marriage and fertility in Palestine using three alternate theories: (1) higher fertility is a political response to existential threat associated with expansion of settler communities (minority status hypothesis), (2) larger numbers of checkpoints in a place isolate it from neighboring places, and narrows accessible marriage market possibly increasing age at marriage (marriage market hypothesis) and (3) for families under stress, responses to both checkpoints and larger settlement populations will be to ‘double down’ on family - an earlier age at marriage and higher fertility within marriage despite fracturing of the marriage market (family security hypothesis). We use data from Palestinian Censuses of 1997 and 2007 and divide the 11 West Bank governorates into 31 distinct geographic areas, distinguishing urban, rural, and refugee camps. We test the hypotheses for women age 10 to 49 years in 2007, controlling for place of residence characteristics in 1997, community marriage and fertility rates in 1997, and change in community level of development from 1997 to 2007. Military checkpoints and settler population penetration in each governorate measure the intensity of the Israeli Occupation. We find evidence consistent with family security hypothesis.
Mining Face-to-Face Interaction Networks using Sociometric Badges: Predicting Productivity in an IT Configuration Task

Social network theories (e.g. Granovetter 1973, Burt 1992) and information richness theory (Daft & Lengel 1987) have both been used independently to understand knowledge transfer in information intensive work settings. Social network theories explain how network structures covary with the diffusion and distribution of information, but largely ignore characteristics of the communication channels (or media) through which information and knowledge are transferred. Information richness theory on the other hand focuses explicitly on the communication channel requirements for different types of knowledge transfer but ignores the population level topology through which information is transferred in a network. This paper aims to bridge these two sets of theories to understand what types of social structures are most conducive to transferring knowledge and improving work performance in face-to-face communication networks. Using a novel set of data collection tools, techniques and methodologies, we were able to record precise data on the face-to-face interaction networks, tonal conversational variation and physical proximity of a group of IT configuration specialists over a one month period while they conducted their work. Linking these data to detailed performance and productivity metrics, we find four main results. First, the face-to-face communication networks of productive workers display very different topological structures compared to those discovered for email networks in previous research. In face-to-face networks, network cohesion is positively correlated with higher worker productivity, while the opposite is true in email communication. Second, network cohesion in face-to-face networks is associated with even higher work performance when executing complex tasks. This result suggests that network cohesion may complement information-rich communication media for transferring the complex or tacit knowledge needed to complete complex tasks. Third, the most effective network structures for latent social networks (those that characterize the network of available communication partners) differ from in-task social networks (those that characterize the network of communication partners that are actualized during the execution of a particular task). Finally, the effect of cohesion is much stronger in face-to-face networks than in physical proximity networks, demonstrating that information flows in actual conversations (rather than mere physical proximity) are driving our results. Our work bridges two influential bodies of research in order to contrast face-to-face network structure with network structure in electronic communication. We also contribute a novel set of tools and techniques for discovering and recording precise face-to-face interaction data in real world work settings.
Mechanism of Electron Conduction in Self‐Assembled Alkanethiol Monolayer Devices

Abstract: Electron tunneling through self‐assembled monolayers (SAMs) of alkanethiols was investigated using nanometer scale devices that allow temperature‐dependent current‐voltage, I(V, T), measurements. The I(V, T) measurement results show, for the first time, temperature‐independent electron transport characteristics, proving direct tunneling as the transport mechanism in alkanethiol SAMs. The measured tunneling currents can be fitted with theoretical calculations using the modified rectangular barrier model of direct tunneling with a barrier height ΦB= 1.42 ± 0.04 eV and a non‐ideal barrier factor α= 0.65 ± 0.01 (that may correspond to effective mass of 0.42 m). From the length‐dependent conduction measurement on different alkanethiols of various lengths, the tunneling current exhibits exponential dependence on the molecular length, d, as I ∝ exp(−βd), where β is a decay coefficient that was found to be bias‐dependent and agrees with the existing theory of direct tunneling. A zero field decay coefficient β0 of 0.79 ± 0.01 Å−1 was obtained.
Graph Edit Distance for Active Graph Matching in Content Based Retrieval Applications

Application of multimedia technologies to visual data, like still images and videos, is receiving an increasing attention especially for the large number of potential innovative solutions which are expected to emerge in the next years. In this context, techniques for retrieval by visual similarity are expected to boost the interest of users through the definition of novel paradigms to access digital repositories of visual data. In this paper, we define a novel model for active graph matching and describe its application to content based retrieval of images. The proposed solution fits with the class of edit distance based techniques and supports active node merging during the graph matching process. A theoretical analysis of the computational complexity of the proposed solution is presented and a prototype system is experimented on the images of two sample image collections.
Splitting in Schizophrenia and Borderline Personality Disorder

Background Splitting describes fragmentation of conscious experience that may occur in various psychiatric disorders. A purpose of this study is to examine relationships between psychological process of splitting and disturbed cognitive and affective functions in schizophrenia and borderline personality disorder (BPD). Methods In the clinical study, we have assessed 30 patients with schizophrenia and 35 patients with BPD. The symptoms of splitting were measured using self-reported Splitting Index (SI). As a measure of semantic memory disorganization we have used verbal fluency test. Other psychopathological symptoms were assessed using Health of the Nation Outcome Scale (HoNOS). Results Main results show that SI is significantly higher in BPD group than in schizophrenia, and on the other hand, verbal fluency is significantly lower in schizophrenia group. Psychopathological symptoms measured by HoNOS are significantly higher in the BPD group than in schizophrenia. Significant relationship was found between verbal fluency and the SI “factor of others” (Spearman r = −0.52, p<0.01) in schizophrenia patients. Conclusions Processes of splitting are different in schizophrenia and BPD. In BPD patients splitting results to mental instability, whereas in schizophrenia the mental fragmentation leads to splitting of associations observed as lower scores of verbal fluency, which in principle is in agreement with Bleuler’s historical concept of splitting in schizophrenia.
De novo protein design using pairwise potentials and a genetic algorithm

One of the major goals of molecular biology is to understand how protein chains fold into a unique 3‐dimensional structure. Given this knowledge, perhaps the most exciting prospect will be the possibility of designing new proteins to perform designated tasks, an application that could prove to be of great importance in medicine and biotechnology. It is possible that effective protein design may be achieved without the requirement for a full understanding of the protein folding process. In this paper a simple method is described for designing an amino acid sequence to fit a given 3‐dimensional structure. The compatibility of a designed sequence with a given fold is assessed by means of a set of statistically determined potentials (including interresidue pairwise and solvation terms), which have been previously applied to the problem of protein fold recognition. In order to generate sequences that best fit the fold, a genetic algorithm is used, whereby the sequence is optimized by a stochastic search in the style of natural selection.
A Case of Acute Pyogenic Sacroiliitis and Bacteremia Caused by Community-Acquired Methicillin-Resistant Staphylococcus aureus

Pyogenic sacroiliitis is a rare osteoarticular infection, occurring most frequently in children and young adults. Diagnosis of the disease is challenging because of a general lack of awareness of the disease and its nonspecific signs and symptoms. Staphylococcus aureus is the most common causative bacteria in pyogenic sacroiliitis. Methicillin-resistant S. aureus (MRSA) has typically been considered a hospital-associated pathogen; however, community-acquired (CA)-MRSA infections are becoming increasingly common in Korea. We report the first domestic case of acute pyogenic sacroiliitis with abscess and bacteremia caused by CA-MRSA. The pathogen carried the type IV-A staphylococcal cassette chromosome mec (SCCmec) without the Panton-Valentine leukocidin (PVL) gene, and was identified as sequence type (ST) 72 by multilocus sequence typing.
Drosophila mutants suggest a strong drive toward complexity in evolution

The view that complexity increases in evolution is uncontroversial, yet little is known about the possible causes of such a trend. One hypothesis, the Zero Force Evolutionary Law (ZFEL), predicts a strong drive toward complexity, although such a tendency can be overwhelmed by selection and constraints. In the absence of strong opposition, heritable variation accumulates and complexity increases. In order to investigate this claim, we evaluate the gross morphological complexity of laboratory mutants in Drosophila melanogaster, which represent organisms that arise in a context where selective forces are greatly reduced. Complexity was measured with respect to part types, shape, and color over two independent focal levels. Compared to the wild type, we find that D. melanogaster mutants are significantly more complex. When the parts of mutants are categorized by degree of constraint, we find that weakly constrained parts are significantly more complex than more constrained parts. These results support the ZFEL hypothesis. They also represent a first step in establishing the domain of application of the ZFEL and show one way in which a larger empirical investigation of the principle might proceed.
The role of Gα O‐mediated signaling in the rostral ventrolateral medulla oblongata in cardiovascular reflexes and control of cardiac ventricular excitability

The heart is controlled by the sympathetic and parasympathetic limbs of the autonomic nervous system with inhibitory signaling mechanisms recruited in both limbs. The aim of this study was to determine the role of inhibitory heterotrimeric G proteins in the central nervous mechanisms underlying autonomic control of the heart and its potential role in arrhythmogenesis. Mice with conditional deletion of the inhibitory heterotrimeric G protein GαO in the presympathetic area of the rostral ventral lateral medulla (RVLM) were generated to determine the role of GαO‐mediated signalling in autonomic control and electrophysiological properties of the heart. GαO deletion within the RVLM was not associated with changes in heart rate (HR) or the arterial blood pressure at rest (home cage, normal behavior). However, exposure to stressful conditions (novel environment, hypoxia, or hypercapnia) in these mice was associated with abnormal HR responses and an increased baroreflex gain when assessed under urethane anesthesia. This was associated with shortening of the ventricular effective refractory period. This phenotype was reversed by systemic beta‐adrenoceptor blockade, suggesting that GαO depletion in the RVLM increases central sympathetic drive. The data obtained support the hypothesis that GαO‐mediated signaling within the presympathetic circuits of the RVLM contributes to the autonomic control of the heart. GαO deficiency in the RVLM has a significant impact on cardiovascular responses to stress, cardiovascular reflexes and electrical properties of the heart.
On the Constituent Attributes of Software and Organizational Resilience

Abstract The conjecture is put forward that a better understanding of resilience may be reached by decomposing it into a number of ancillary constituent properties, in the same way as a better insight into system dependability was obtained by breaking it down into safety, availability, reliability, and other sub-properties. Three of the main sub-properties of resilience proposed here refer respectively to the ability to perceive environmental changes; to understand the implications introduced by those changes; and to plan and enact adjustments intended to improve the system–environment fit. A fourth property characterizes the way the above abilities manifest themselves in computer systems. The four properties are then analyzed in three families of case studies, each consisting of three software systems that embed different resilience methods. Our major conclusion is that reasoning in terms of our resilience sub-properties may help reveal the characteristics and, in particular, the limitations of classic methods and tools meant to achieve system and organizational resilience. It is suggested that this method may be a prelude to meta-resilient systems, which are able to adjust optimally their own resilience with respect to changing environmental conditions.
Physical Properties of Human Mycoplasma Species

Kim, Kwang S. (University of North Carolina, Chapel Hill), Wallace A. Clyde, Jr., and Floyd W. Denny. Physical properties of human mycoplasma species. J. Bacteriol. 92:214–219. 1966. —Studies were made of the comparative morphology and stability of five Mycoplasma species of human origin (M. hominis type 1, M. salivarium, M. fermentans, M. pneumoniae, M. pharyngis). Broth-cultivated organisms were examined by electron microscopy to determine their relative appearance after uniform processing, including fixation-drying with formaldehyde vapor. M. pneumoniae was characterized by the occurrence of 250- to 300-mμ spheres in clusters, and M. pharyngis by the appearance of filaments 120 mμ by 1.5 to 8 μ; the remaining species revealed a variety of structures, including spheres, rings, and short filaments. To complement these findings, the effect of physical stresses on viability of the mycoplasmas was measured by exposing the organisms to heat (in saline), osmotic variations (in sucrose), and sonic oscillation and repetitive freeze-thawing (in culture medium). M. pneumoniae was most resistant to heat, vibration, and freeze-thawing; M. pharyngis was most sensitive to heart and vibration, but was least affected by osmotic changes. The remaining organisms assumed intermediate positions. The type-related variations in relative morphology and stability suggest differing physical attributes of the mycoplasmas studied, supporting taxonomic differentiation of the five species based on metabolic and immunological criteria.
On Schwinger pair creation in gravity and in closed superstring theory

We investigate the Schwinger pair creation process in the context of gravitational models with the back reaction of the electric field included in the geometry. The background is also an exact solution of type II superstring theory, where the electric field arises by Kaluza-Klein reduction. We obtain a closed formula for the pair creation rate that incorporates the gravitational back reaction. At weak fields it has the same structure as the general Schwinger formula, albeit pairs are produced by a combination of Schwinger and Unruh effect, the latter due to the presence of a Rindler horizon. In four spacetime dimensions, the rate becomes constant at strong electric fields. For states with mass of Kaluza-Klein origin, the rate has a power-like dependence in the electric field, rather than the familiar (non-perturbative) exponential dependence. We also reproduce the same formula from the string partition function for winding string states. Finally, we comment on the generalization to excited string states.