Miracle-dz/UniFAR-FTUs huggingface dataset:
Trace-based debugging for advanced-dispatching programming languages

Advanced-dispatching programming languages allow to implicitly alter the behaviour of a program, depending on run-time program context. While this improves modularity, it also impedes comprehensibility. The use of advanced-dispatching programming languages can give rise to complex debugging scenarios, which cannot efficiently be resolved with traditional debugging approaches such as breakpoint-based debugging. Therefore, tool support for analysing the full history of runtime behaviour of advanced-dispatching programs is of importance for efficient debugging. In this paper, we characterise debugging scenarios for which existing work does not apply well, because they require access to the program execution history for efficient resolution. We present our design and implementation of a trace-based debugger for advanced-dispatching that supports such debugging scenarios efficiently. Our approach is the first one based on an XML-representation of the execution trace, giving rise to using very powerful standard tools such as the XQuery language for searching and navigating the trace, or scalable visualisations such as tree-maps.
Dependent rounding and its applications to approximation algorithms

We develop a new randomized rounding approach for fractional vectors defined on the edge-sets of bipartite graphs. We show various ways of combining this technique with other ideas, leading to improved (approximation) algorithms for various problems. These include:---low congestion multi-path routing;---richer random-graph models for graphs with a given degree-sequence;---improved approximation algorithms for: (i) throughput-maximization in broadcast scheduling, (ii) delay-minimization in broadcast scheduling, as well as (iii) capacitated vertex cover; and---fair scheduling of jobs on unrelated parallel machines.
A space-time coding modem for high-data-rate wireless communications

This paper presents the theory and practice of a new advanced modem technology suitable for high-data-rate wireless communications and presents its performance over a frequency-flat Rayleigh fading channel. The new technology is based on space-time coded modulation (STCM) with multiple transmit and/or multiple receive antennas and orthogonal pilot sequence insertion (O-PSI). In this approach, data is encoded by a space-time (ST) channel encoder and the output of the encoder is split into N streams to be simultaneously transmitted using N transmit antennas. The transmitter inserts periodic orthogonal pilot sequences in each of the simultaneously transmitted bursts. The receiver uses those pilot sequences to estimate the fading channel. When combined with an appropriately designed interpolation filter, accurate channel state information (CSI) can be estimated for the decoding process. Simulation results of the proposed modem, as applied to the IS-136 cellular standard, are presented. We present the frame error rate (FER) performance results as a function of the signal-to-noise ratio (SNR) and the maximum Doppler frequency, in the presence of timing and frequency offset errors. Simulation results show that for a 10% FER, a 32-state eight-phase-shift keyed (8-PSK) ST code with two transmit and two receive antennas can support data rates up to 55.8 kb/s on a 30-kHz channel, at an SNR of 11.7 dB and a maximum Doppler frequency of 180 Hz. Simulation results for other codes and other channel conditions are also provided. We also compare the performance of the proposed STCM scheme with delay diversity schemes and conclude that STCM can provide significant SNR improvement over simple delay diversity.
Asthma, Chronic Obstructive Pulmonary Disease, and Mortality in the U.S. Population

Background: COPD and asthma are common diseases in the U.S. population and can coexist. Our goal was to determine the prevalence of self-reported, physician-diagnosed asthma and COPD in a sample of the U.S. population and their association with lung function impairment and mortality. Methods: We used baseline data from NHANES III and the follow-up mortality data. We used logistic regression and Cox Proportional Hazards models, adjusting for age, sex, race/ethnicity, education level, smoking status, and disease stage. Results: The sample consisted of 15,203 subjects, of whom 4,542 died during the follow-up period. Coexisting COPD and asthma was reported by 357 (2.7%), COPD by 815 (5.3%), and asthma by 709 (5.3%). Subjects with both conditions had a higher proportion of obstruction (30.9%) than those with COPD (24.3%), asthma (13.3%), or no lung disease (5.4%). In survival models adjusting for all factors except baseline lung function, coexisting COPD and asthma had the highest risk for mortality (Hazard Ratio [HR] 1.83, 95% confidence interval [CI] 1.34, 2.49), followed by COPD only (HR 1.44, 95% CI 1.28, 1.62), and asthma only (HR 1.16, 95% CI 0.94, 1.42). These affects were attenuated after controlling for baseline lung function: coexisting asthma and COPD (HR 1.45, 95% CI 1.06, 1.98), COPD only (1.28, 95% CI 1.13, 1.45), and asthma only (HR 1.04, 95% CI 0.85, 1.27). Conclusion: In this analysis, subjects who report coexisting asthma and COPD have a higher risk of obstruction on spirometry and a higher risk of death during follow-up.
Lightweight authentication of linear algebraic queries on data streams

We consider a stream outsourcing setting, where a data owner delegates the management of a set of disjoint data streams to an untrusted server. The owner authenticates his streams via signatures. The server processes continuous queries on the union of the streams for clients trusted by the owner. Along with the results, the server sends proofs of result correctness derived from the owner's signatures, which are easily verifiable by the clients. We design novel constructions for a collection of fundamental problems over streams represented as linear algebraic queries. In particular, our basic schemes authenticate dynamic vector sums and dot products, as well as dynamic matrix products. These techniques can be adapted for authenticating a wide range of important operations in streaming environments, including group by queries, joins, in-network aggregation, similarity matching, and event processing. All our schemes are very lightweight, and offer strong cryptographic guarantees derived from formal definitions and proofs. We experimentally confirm the practicality of our schemes.
Induction of perlecan gene expression precedes amyloid formation during experimental murine AA amyloidogenesis.

BACKGROUND In a murine model of AA amyloidosis, it has been demonstrated that perlecan, the basement membrane heparan sulfate proteoglycan, is co-deposited with AA amyloid as it forms in various tissues. The objectives of this study were to determine whether the accumulation of perlecan during amyloidogenesis is associated with induction of perlecan gene expression and, if so, to define the temporal relationship of this induction to the onset of amyloid formation. EXPERIMENTAL DESIGN Accelerated splenic AA amyloidosis was stimulated in mice by concomitant administration of subcutaneous silver nitrate as an inflammatory stimulus and amyloid-enhancing factor. A kinetic analysis of splenic perlecan mRNA levels during amyloid formation in the spleen was conducted using a reverse transcription-polymerase chain reaction assay. Amyloid deposits were detected histochemically with the Congo red stain and by immunohistochemistry using anti-AA antisera. RESULTS Perlecan mRNA levels increased significantly during amyloidogenesis, increasing 4.1-fold within 72 hours of the amyloidogenic stimulus and subsequently falling to steady-state levels. A 2.0-fold induction of perlecan mRNA occurred by 24 hours post-stimulation, a time at which amyloid was not detectable by either histochemistry or immunohistochemistry. In contrast, control animals administered either the inflammatory stimulus or AEF alone showed no significant change in perlecan mRNA levels. CONCLUSIONS Increased perlecan mRNA levels account, at least in part, for the accumulation of perlecan in murine splenic AA amyloid deposits. This induction of perlecan gene expression occurs before the onset of amyloid formation, supporting a role for perlecan in the earliest stages of amyloid fibrillogenesis.
Assuring application-level correctness against soft errors

Traditionally, research in fault tolerance has required architectural state to be numerically perfect for program execution to be correct. However, in many programs, even if execution is not 100% numerically correct, the program can still appear to execute correctly from the user's perspective. To quantify user satisfaction, application-level fidelity metrics (such as PSNR) can be used. The output for such applications is defined to be correct if the fidelity metrics satisfy a certain threshold. However, such applications still contain instructions whose outputs are critical — i.e. their correctness decides if the overall quality of the program output is acceptable. In this paper, we present an analysis technique for identifying such critical program segments. More importantly, our technique is capable of guaranteeing application-level correctness through a combination of static analysis and runtime monitoring. Our static analysis consists of data flow analysis followed by control flow analysis to find static critical instructions which affect several instructions. Critical instructions are further refined into likely non-critical and likely critical sets in a profiling phase. At runtime, we use a monitoring scheme to monitor likely non-critical instructions and take remedial actions if some likely non-critical instructions become critical. Based on this analysis, we minimize the number of instructions that are duplicated and checked at runtime using a software-based fault detection and recovery technique [20]. Put together, our approach can lead to 22% average energy savings for multimedia applications while guaranteeing application-level correctness, when compared to a recent work [9], which cannot guarantee application-level correctness. Comparing to the approach proposed in [20] which guarantees both application-level and numerical correctness, our method achieves 79% energy reduction.
High performance single supply CMOS inverter level up shifter for multi-supply voltages domains

A single supply CMOS inverter level shifter (ssqc- ls) for upconverting signals from 0.4V-1V logic level range up to 1.1V power supply domain is introduced. For guaranteing a low energy consumption, the proposed shifter is based on topological modifications of the structure qc-level shifter reported in [1]. For 0.5V input square wave switching at 500MHz, the inverter level shifter ssqc-ls using 1.2V of power supply voltage achieves a 60% of Figure of Merit improvement in comparison against jy-ls [8] with a dual power supply voltage of 0.6V and 1.2V. Post-layout simulation results shown that ssqc-ls reaches a propagation delay of 0.75ns, an energy consumption of only 2.3pJ, and an energy- delay product of 1.73pJns for a capacitive loading condition of 950fF.
Structure of Human Microsomal Cytochrome P450 2C8

A 2.7-Å molecular structure of human microsomal cytochrome P450 2C8 (CYP2C8) was determined by x-ray crystallography. The membrane protein was modified for crystallization by replacement of the hydrophobic N-terminal transmembrane domain with a short hydrophilic sequence before residue 28. The structure of the native sequence is complete from residue 28 to the beginning of a C-terminal histidine tag used for purification. CYP2C8 is one of the principal hepatic drug-metabolizing enzymes that oxidizes therapeutic drugs such as taxol and cerivastatin and endobiotics such as retinoic acid and arachidonic acid. Consistent with the relatively large size of its preferred substrates, the active site volume is twice that observed for the structure of CYP2C5. The extended active site cavity is bounded by the β1 sheet and helix F′ that have not previously been implicated in substrate recognition by mammalian P450s. CYP2C8 crystallized as a symmetric dimer formed by the interaction of helices F, F′, G′, and G. Two molecules of palmitic acid are bound in the dimer interface. The dimer is observed in solution, and mass spectrometry confirmed the association of palmitic acid with the enzyme. This novel finding identifies a peripheral binding site in P450s that may contribute to drug-drug interactions in P450 metabolism.
eZinCh-2: A Versatile, Genetically Encoded FRET Sensor for Cytosolic and Intraorganelle Zn2+ Imaging

Zn2+ plays essential and diverse roles in numerous cellular processes. To get a better understanding of intracellular Zn2+ homeostasis and the putative signaling role of Zn2+, various fluorescent sensors have been developed that allow monitoring of Zn2+ concentrations in single living cells in real time. Thus far, two families of genetically encoded FRET-based Zn2+ sensors have been most widely applied, the eCALWY sensors developed by our group and the ZapCY sensors developed by Palmer and co-workers. Both have been successfully used to measure cytosolic free Zn2+, but distinctly different concentrations have been reported when using these sensors to measure Zn2+ concentrations in the ER and mitochondria. Here, we report the development of a versatile alternative FRET sensor containing a de novo Cys2His2 binding pocket that was created on the surface of the donor and acceptor fluorescent domains. This eZinCh-2 sensor binds Zn2+ with a high affinity that is similar to that of eCALWY-4 (Kd = 1 nM at pH 7.1), while displaying a substantially larger change in emission ratio. eZinCh-2 not only provides an attractive alternative for measuring Zn2+ in the cytosol but was also successfully used for measuring Zn2+ in the ER, mitochondria, and secretory vesicles. Moreover, organelle-targeted eZinCh-2 can also be used in combination with the previously reported redCALWY sensors to allow multicolor imaging of intracellular Zn2+ simultaneously in the cytosol and the ER or mitochondria.
Agricultural risk and the spread of religious communities

Building on the idea that members of religious communities insure each other against some idiosyncratic risks, we argue that religious communities should be more widespread where populations face greater common risk. Our empirical analysis exploits rainfall risk as a source of common agricultural risk in the nineteenth-century United States. We show that a greater share of the population was organized into religious communities in counties with greater rainfall risk. The link between rainfall risk and membership in religious communities is stronger among more agricultural counties and counties exposed to greater rainfall risk during the growing season.
Patient classification based on expanded query using 5-gram collocation and binary tree

Patients in rural India express their discomfort using keyword as query due to their lack of knowledge about the intended domain. Therefore, there is no scope of automatic revision of the query using feedback mechanism, unlike the existing query expansion methods. The paper aims at developing a primary level disease diagnosis system for the patients of rural India by expanding the query using 5-gram collocation model. First a string of five co-occurred words with respect to each query are obtained by consulting several medical documents. We call the string of five terms as bag of symptom (BoS), representing a concept. For each query there is multiple BoSs from which we select ten only based on their rank, measured using Log-likelihood ratio. However, all the terms in the BoS may not represent the disease symptom but semantically related concept similar to the symptoms of the symptom vocabulary (SV). We propose a novel binary tree based approach to calculate the degree of similarity (DoS) between the terms in the BoS and the symptoms in the SV using topology of the tree and term frequency-inverse document frequency (tf-idf) of the symptoms. The SV with respect to each BoS is encoded with DoS value and framed as feature vectors, which are mostly sparse. To remove sparsity in the feature vectors we apply singular value decomposition (SVD) method. Finally, the patients are classified into four probable diseases using 10-fold cross validation technique where the SV consists optimum no. of symptoms for such diseases. We classify pregnant women separately into two probable diseases and each of the cases the system shows satisfactory performance.
Critical Review of Need for Achievement Effect on the Job Performance-Job Attitude Relationship

Sebagian besar studi empiris tentang perilaku kerja-sikap kerja difokuskan pada hubungan antara kinerja dan sikap kerja tanpa mempertimbangkan faktor lain yang mungkin mempengaruhi hubungan tersebut. Kebutuhan atas pencapaian merupakan suatu variabel disposisional yang berpotensi untuk memoderasi asosiasi antara kinerja dan sikap kerja. Studi yang dilakukan oleh Steers (1975) ini sengaja dipilih karena merupakan studi awal yang menguji pengaruh kebutuhan atas pencapaian pada hubungan antara kinerja dengan sikap kerja, dalam hal ini keterlibatan kerja dan kepuasan kerja. Kelemahan utama studi ini terletak pada metode penelitian terkait dengan operasionalisasi dan pengukuran variabel-variabel yang diteliti. Metode pemilihan sampel, pengajuan masalah, dan ketiadaan simpulan, merupakan kelemahan lain studi ini. Terlepas dari kelemahan-kelemahan tersebut, studi ini memberi kontribusi berharga pada ilmu keperilakuan karena mempertimbangkan peranan valen dan instrumentalitas dalam hubungan perilaku kerjamsikap kerja.
The Effect of a Noise Reducing Test Accommodation on Elementary Students with Learning Disabilities

Researchers in the fields of cognitive psychology and education have been studying the negative effects of noise on human performance for almost a century. A new empirical study that builds upon past relevant research on (1) test accommodations and (2) auditory distraction and academic performance was conducted with elementary age students. Reading comprehension tasks were completed by students with and without learning disabilities while wearing and not wearing noise–reducing headphones. Results of three independent statistical analyses are presented. Implications, limitations, and the need for future research are also discussed.
Solving very large RWA data instances

While the Routing and Wavelength Assignment (RWA) has been widely studied, few studies attempt to solve realistic size instances, namely, with 150 wavelengths per fiber and a few hundred nodes. Indeed, state of the art is closer to around 20 nodes and 30 wavelengths, regardless of what the authors consider, heuristics or exact methods with very few exceptions. In this paper, we are interested in reducing the gap between realistic data sets and testbed instances that are often used, using exact methods. Even if exact methods may fail to solve in reasonable time very large instances, they however output bounds on the accuracy of the heuristic solutions. The novelty of our work is to exploit the observations that optimal solutions contain a very large number of lightpaths associated with shortest paths or k shortest paths with a small k. We propose different RWA algorithms that lead to solve exactly or near exactly much larger instances than in the literature with up to 150 wavelengths and 50 nodes.
The role of fire in the mid-Holocene arrival and expansion of lodgepole pine (Pinus contorta var. latifolia Engelm. ex S. Watson) in Yukon, Canada

In north-west Canada, Pinus contorta (lodgepole pine) has been migrating northwards and westwards for millennia. Its regeneration is currently enhanced by fire, which may act as a trigger for local population expansion. Using Holocene charcoal records from four small (<10 ha) lakes in southern Yukon, we investigated the relationship between long-term Pinus population dynamics and fire. Fossil stomata extracted from dated lake sediments indicate pine was present at low densities in southern Yukon forests by ~6000 cal. yr BP. At each site, the main population expansion (indicated by an increase in Pinus pollen from <5% to values as high as 60%) occurred 2000–>4000 years after the first local appearance of Pinus, suggesting a long period of stasis at low densities. Population increases – based on pollen accumulation rates (PARs) – occurred at different times at the four sites. Estimated expansion periods were ~2500–800 years, and population doubling times were ~150–600 years, similar to previous estimates. Estimated fire return intervals (FRIs) fluctuated over time. At all sites, the Pinus expansion began during a phase with a relatively short FRI, but only one difference between the mean FRIs before and during the Pinus rise was statistically distinguishable. Nor was the subsequent higher abundance of pine associated with shorter FRIs. It is unlikely that regional pine expansion is primarily linked to changes in climate or a climate-mediated fire regime, although expansion may have been triggered at individual sites during a period of high fire frequency. The long period of stasis at low population densities suggests intrinsic control of population growth; possibly Pinus expansion was initially constrained by lowered reproductive fitness (Allee effect) and/or interaction with local site-based factors.
Physical Determinants of Phytoplankton Production, Algal Stoichiometry, and Vertical Nutrient Fluxes

Most phytoplankters face opposing vertical gradients in light versus nutrient supplies but have limited capacities for vertical habitat choice. We therefore explored a dynamical model of negatively buoyant algae inhabiting a one‐dimensional water column to ask how water column depth and turbulence constrain total (areal) phytoplankton biomass. We show that the population persistence boundaries in water column depth–turbulence space are set by sinking losses and light limitation but that nutrients are most limiting to total biomass in water columns that are neither too shallow or too weakly mixed (where sinking losses prevail) nor too deep and turbulent (where light limitation prevails). In shallow waters, the most strongly limiting process is nutrient influx to the bottom of the water column (e.g., from sediments). In deep waters, the most strongly limiting process is turbulent upward transport of nutrients to the photic zone. Consequently, the highest total biomasses are attained in turbulent waters at intermediate water column depths and in deep waters at intermediate turbulences. These patterns are insensitive to the assumption of fixed versus flexible algal carbon‐to‐nutrient stoichiometry, and they arise irrespective of whether the water column is a surface layer above a deep water compartment or has direct contact with sediments.
Determination of RNA structure and thermodynamics.

PHYLOGENETIC AND MUTATIONAL ANALYSES . 258 Natural Sequence Variability 258 Artificial Phylogeny . 259 Random Mutations and Specific Selection . 260 Functional Group Mutations . 260 OPTICAL SPECTROSCOPY . 260 Absorbance . 260 Circular Dichroism . 263 Fluorescence . 263