Miracle-dz/UniFAR-FTUs huggingface dataset:
Changing Perspectives on Pearly Mussels, North America's Most Imperiled Animals

Abstract Pearly mussels (Unionacea) are widespread, abundant, and important in freshwater ecosystems around the world. Catastrophic declines in pearly mussel populations in North America and other parts of the world have led to a flurry of research on mussel biology, ecology, and conservation. Recent research on mussel feeding, life history, spatial patterning, and declines has augmented, modified, or overturned long-held ideas about the ecology of these animals. Pearly mussel research has begun to benefit from and contribute to current ideas about suspension feeding, life-history theory, metapopulations, flow refuges, spatial patterning and its effects, and management of endangered species. At the same time, significant gaps in understanding and apparent paradoxes in pearly mussel ecology have been exposed. To conserve remaining mussel populations, scientists and managers must simultaneously and aggressively pursue both rigorous research and conservation actions.
Software behavior oriented parallelization

Many sequential applications are difficult to parallelize because of unpredictable control flow, indirect data access, and input-dependent parallelism. These difficulties led us to build a software system for behavior oriented parallelization (BOP), which allows a program to be parallelized based on partial information about program behavior, for example, a user reading just part of the source code, or a profiling tool examining merely one or few executions. The basis of BOP is programmable software speculation, where a user or an analysis tool marks possibly parallel regions in the code, and the run-time system executes these regions speculatively. It is imperative to protect the entire address space during speculation. The main goal of the paper is to demonstrate that the general protection can be made cost effective by three novel techniques: programmable speculation, critical-path minimization, and value-based correctness checking. On a recently acquired multi-core, multi-processor PC, the BOP system reduced the end-to-end execution time by integer factors for a Lisp interpreter, a data compressor, a language parser, and a scientific library, with no change to the underlying hardware or operating system.
The "Best" Algorithm for solving Stochastic Mixed Integer Programs

We present a new algorithm for solving two-stage stochastic mixed-integer programs (SMIPs) having discrete first-stage variables, and continuous or discrete second-stage variables. For a minimizing SMIP, the BEST algorithm (1) computes an upper Bound on the optimal objective value (typically a probabilistic bound), and identifies a deterministic lower-bounding function, (2) uses the bounds to Enumerate a set of first-stage solutions that contains an optimal solution with pre-specified confidence, (3) for each first-stage solution, Simulates second-stage operations by repeatedly sampling random parameters and solving the resulting model instances, and (4) applies statistical Tests (e.g., "screening procedures") to the simulated outcomes to identify a near-optimal first-stage solution with pre-specified confidence. We demonstrate the algorithm's performance on a stochastic facility-location problem
Classification Tree Methods for Analysis of Mesoscale Distribution of Ixodes ricinus (Acari: Ixodidae) in Trentino, Italian Alps

Prevalenza di Bor-relia burgodoferi in Ixodes ricinus in alcune aree del trentino. malat-tie infettive nell'arco alpino. Analisi retrospettiva di 75 pazienti con manifestazioni cutanee di malat-tia di Lyme.
Monolithic mode locking of long cavity GaAs-AlGaAs semiconductor lasers

A description is presented of active and hybrid mode locking of long 0.85- mu m monolithic semiconductor lasers. Active mode locking at 8.6 GHz is achieved by applying an RF modulation (with or without positive bias) to a short section of the cavity through a separate contact. By reverse biasing the contact and applying the RF modulation, hybrid mode locking is achieved, and in this case pulses of 16 ps duration are measured by a streak camera; although with some chirp, as indicated by a time-bandwidth product of 2.7. Partial passive mode locking is also achieved by application of a reverse bias to the split contact. <<ETX>>
A Conserved Coatomer-related Complex Containing Sec13 and Seh1 Dynamically Associates With the Vacuole in Saccharomyces cerevisiae*

The presence of multiple membrane-bound intracellular compartments is a major feature of eukaryotic cells. Many of the proteins required for formation and maintenance of these compartments share an evolutionary history. Here, we identify the SEA (Seh1-associated) protein complex in yeast that contains the nucleoporin Seh1 and Sec13, the latter subunit of both the nuclear pore complex and the COPII coating complex. The SEA complex also contains Npr2 and Npr3 proteins (upstream regulators of TORC1 kinase) and four previously uncharacterized proteins (Sea1–Sea4). Combined computational and biochemical approaches indicate that the SEA complex proteins possess structural characteristics similar to the membrane coating complexes COPI, COPII, the nuclear pore complex, and, in particular, the related Vps class C vesicle tethering complexes HOPS and CORVET. The SEA complex dynamically associates with the vacuole in vivo. Genetic assays indicate a role for the SEA complex in intracellular trafficking, amino acid biogenesis, and response to nitrogen starvation. These data demonstrate that the SEA complex is an additional member of a family of membrane coating and vesicle tethering assemblies, extending the repertoire of protocoatomer-related complexes.
Formal Verification of a Simple Automated Negotiation Protocol

Negotiation is a complex human activity and even in its most basic form consists of three elements: communication, strategy and bid evaluation. The elements are exactly the same in automated negotiation. In this paper we present four possible approaches for bid evaluation and strategy but we mainly focus on the communication aspect of the negotiation. Communication lends itself well to be specified and modeled as a protocol, so we introduce a basic automated negotiation protocol which we simulate and verify using PROMELA and the SPIN model checker.
Exploring the avian gut microbiota: current trends and future directions

Birds represent a diverse and evolutionarily successful lineage, occupying a wide range of niches throughout the world. Like all vertebrates, avians harbor diverse communities of microorganisms within their guts, which collectively fulfill crucial roles in providing the host with nutrition and protection from pathogens. Across the field of avian microbiology knowledge is extremely uneven, with several species accounting for an overwhelming majority of all microbiological investigations. These include agriculturally important birds, such as chickens and turkeys, as well as birds of evolutionary or conservation interest. In our previous study we attempted the first meta-analysis of the avian gut microbiota, using 16S rRNA gene sequences obtained from a range of publicly available data sets. We have now extended our analysis to explore the microbiology of several key species in detail, to consider the avian microbiota within the context of what is known about other vertebrates, and to identify key areas of interest in avian microbiology for future study.
Inferring Human Upper Body Motion Using Belief Propagation

We present an algorithm for automatic inference of human upper body motion in a natural scene. A graph model is proposed for inferring human upper body motion, and motion inference is posed as a mapping problem between state nodes in the graph model and features in image patches. A multiple-frame inference algorithm is proposed to combine both structural and temporal constraints in human upper body motion. Belief propagation and dynamic programming algorithms are utilized for Bayesian inference in this graph. We also present a method for capturing constraints of human body configuration under different view angles. The algorithm is applied in a prototype system that can automatically detect upper body motion from videos, without manual initialization of body parts. We present evaluation results of our algorithm.
Positive end-expiratory pressure titration in acute respiratory distress syndrome patients: Impact on right ventricular outflow impedance evaluated by pulmonary artery Doppler flow velocity measurements

Objective Positive end-expiratory pressure (PEEP) titration in acute respiratory distress syndrome patients remains debatable. We used two mechanical approaches, calculation of the compliance of the respiratory system and determination of the lower inflexion point of the pressure-volume curve of the respiratory system, to identify specific PEEPs (PEEPS and PEEPA) whose impact on right ventricular (RV) outflow was compared with Doppler analysis of pulmonary artery flow velocity. Design Prospective, open, clinical study. Setting Medical intensive care unit of a university hospital. Patients Sixteen consecutive ventilator-dependent acute respiratory distress syndrome patients. Interventions Two PEEPs were determined: PEEPS was the highest PEEP associated with the highest value of respiratory compliance, and PEEPA was the coordinate of the lower inflexion point of the inspiratory pressure-volume curve on the pressure axis plus 2 cm H2O. Measurements and Main Results We observed a large difference between the two PEEPs, with PEEPA (13 + 4 cm H2O) > PEEPS (6 + 3 cm H2O). Changes in RV outflow impedance produced by tidal ventilation with zero end-expiratory pressure (ZEEP) and after application of these two PEEPs were assessed by Doppler study of pulmonary artery flow velocity obtained by a transesophageal approach, with particular reference to the end-expiratory and end-inspiratory pulmonary artery velocity-time integral, as reflecting RV stroke output, and mean acceleration as reflecting RV outflow impedance during an unchanged flow period. A significant inspiratory reduction in pulmonary artery velocity-time integral (from 11.8 + 0.3 to 10.0 + 0.3 cm) and mean acceleration (from 11.9 + 0.9 to 8.0 + 0.9 m/sec2) was observed with ZEEP, showing a reduction in RV stroke index (from 29.0 + 0.9 to 26.0 + 0.6 cm3/m2) by a sudden increase in outflow impedance during tidal ventilation. Application of PEEPA, which improved Pao2 (102 + 40 vs. 65 + 18 torr with ZEEP), worsened the inspiratory drop in RV stroke index (21.6 + 0.8 cm3/m2), resulting in a significant reduction in cardiac index compared with ZEEP (from 3.0 + 1.0 to 2.7 + 1.1). Application of PEEPS, which also significantly improved Pao2 (81 + 21 torr), was associated with a lesser impact on RV outflow impedance (inspiratory mean acceleration: 9.5 + 1 m/sec2) and cardiac index (3.2 + 1.0) than PEEPA. Conclusion RV outflow impedance evaluated by the Doppler technique appeared sensitive to PEEP titration. Application of PEEPA worsened RV systolic function impairment produced by tidal ventilation. Conversely, application of PEEPS reduced RV systolic function impairment, suggesting an association with a lower pulmonary vascular resistance.
TiML: a functional language for practical complexity analysis with invariants

We present TiML (Timed ML), an ML-like functional language with time-complexity annotations in types. It uses indexed types to express sizes of data structures and upper bounds on running time of functions; and refinement kinds to constrain these indices, expressing data-structure invariants and pre/post-conditions. Indexed types are flexible enough that TiML avoids a built-in notion of ≴size,≵ and the programmer can choose to index user-defined datatypes in any way that helps her analysis. TiML's distinguishing characteristic is supporting highly automated time-bound verification applicable to data structures with nontrivial invariants. The programmer provides type annotations, and the typechecker generates verification conditions that are discharged by an SMT solver. Type and index inference are supported to lower annotation burden, and, furthermore, big-O complexity can be inferred from recurrences generated during typechecking by a recurrence solver based on heuristic pattern matching (e.g. using the Master Theorem to handle divide-and-conquer-like recurrences). We have evaluated TiML's usability by implementing a broad suite of case-study modules, demonstrating that TiML, though lacking full automation and theoretical completeness, is versatile enough to verify worst-case and/or amortized complexities for algorithms and data structures like classic list operations, merge sort, Dijkstra's shortest-path algorithm, red-black trees, Braun trees, functional queues, and dynamic tables with bounds like m n logn. The learning curve and annotation burden are reasonable, as we argue with empirical results on our case studies. We formalized TiML's type-soundness proof in Coq.
Altered kinetics and benzodiazepine sensitivity of a GABAA receptor subunit mutation [γ2(R43Q)] found in human epilepsy

The γ-aminobutyric acid type A (GABAA) receptor mediates fast inhibitory synaptic transmission in the CNS. Dysfunction of the GABAA receptor would be expected to cause neuronal hyperexcitability, a phenomenon linked with epileptogenesis. We have investigated the functional consequences of an arginine-to-glutamine mutation at position 43 within the GABAA γ2-subunit found in a family with childhood absence epilepsy and febrile seizures. Rapid-application experiments performed on receptors expressed in HEK-293 cells demonstrated that the mutation slows GABAA receptor deactivation and increases the rate of desensitization, resulting in an accumulation of desensitized receptors during repeated, short applications. In Xenopus laevis oocytes, two-electrode voltage-clamp analysis of steady-state currents obtained from α1β2γ2 or α1β2γ2(R43Q) receptors did not reveal any differences in GABA sensitivity. However, differences in the benzodiazepine pharmacology of mutant receptors were apparent. Mutant receptors expressed in oocytes displayed reduced sensitivity to diazepam and flunitrazepam but not the imidazopyridine zolpidem. These results provide evidence of impaired GABAA receptor function that could decrease the efficacy of transmission at inhibitory synapses, possibly generating a hyperexcitable neuronal state in thalamocortical networks of epileptic patients possessing the mutant subunit.
On the stochastic calculus method for spins systems

In this note we show how to generalize the stochastic calculus method introduced by Comets and Neveu [Comm. Math. Phys. 166 (1995) 549-564] for two models of spin glasses, namely, the SK model with external field and the perceptron model. This method allows to derive quite easily some fluctuation results for the free energy in those two cases.
Millimeter-wave base station for mobile broadband communication

In this paper a millimeter-wave base station operating at 28GHz for mobile communication is introduced. This base station employs 64-elements antenna phased-array to enable adaptive beamforming required for mobile communication. The phased-array is constructed of sub-arrays for optimal trade-off between performance and required coverage and beamforming capability. The phased array antenna is integrated with the transceivers on the same printed circuit board (PCB) using industry standard manufacturing process to minimize the cost and routing loss. The achieved link budget fulfills the requirements of the LOS and NLOS mobile communication in this band for distances in excess of 1Km. The field measurements depict an end-to-end EVM of better than -24dB for a 16QAM OFDM signal with 500MHz bandwidth (BW).
Progress in heart failure Management? Lessons from the real world.

In recent years, we have learned a great deal about the pathophysiology of heart failure, and we have demonstrated a significant potential for improved clinical outcomes with medical treatments. However, it is important to continually gauge the impact that this incremental knowledge has had on health outcomes in the real world, within populations beyond those enrolled in clinical trials. The study by MacIntyre et al,1 which examines 66 547 consecutive patients with first-time admissions for heart failure in Scotland, provides an important new look at the population of patients with this condition. It offers an opportunity to grade our accomplishments and to identify new approaches required to improve outcomes further. This group studied an elderly population (median age, 72 years in men and 78 years in women), evenly distributed between the sexes, with a poor prognosis (1-year mortality, 44.5%). However, the authors identified modest but encouraging improvement in outcomes over the 10-year observation period. In these findings, we see reason for optimism but also reason for concern that our clinical trials are leaving gaps in our knowledge and are not realizing their full potential for translation into improved public health. For their analysis, MacIntyre et al1 used an imperfect, yet unique and valuable national database. Databases derived from clinical trials or registries2 have the advantage of containing more detailed clinical information; however, the selection process inherent in their construction limit their usefulness in providing a true reflection of heart failure across the population. Furthermore, no such information set has been accumulated over a time frame sufficient to judge longitudinal changes in outcome. Administrative databases, although limited in their clinical content, may have less of a selection bias, and they can provide uniform information across a broad population over a long time frame. In the United States, the …
Managing application level elasticity and availability

Elasticity and availability are two features associated with the cloud. Existing solutions focus on providing both at the level of the virtual infrastructure through virtual machines (VMs), their restart, addition, and removal as needed. These assume a specific application design paradigm, which equates the application and its workload to the VM. High-availability applications are typically composed of redundant components that recover from failures through state-full failover orchestrated by a middleware (MW). For such applications handling elasticity purely through addition and removal of VMs is not sufficient, the application level also needs to be considered. This requires solutions that coordinate the availability and elasticity management at the application level. In this paper we propose a solution in the context of the Service Availability Forum (SAF) defined MW. It manages the application level elasticity through the manipulation of the application configuration used by the MW to ensure service availability. This in turn triggers the MW to change the workload distribution in the system.
Proline metabolism and cancer: emerging links to glutamine and collagen

Purpose of reviewProline metabolism impacts a number of regulatory targets in both animals and plants and is especially important in cancer. Glutamine, a related amino acid, is considered second in importance only to glucose as a substrate for tumors. But proline and glutamine are interconvertible and linked in their metabolism. In animals, proline and glutamine have specific regulatory functions and their respective physiologic sources. A comparison of the metabolism of proline and glutamine would help us understand the importance of these two nonessential amino acids in cancer metabolism. Recent findingsThe regulatory functions of proline metabolism proposed 3 decades ago have found relevance in many areas. For cancer, these functions play a role in apoptosis, autophagy and in response to nutrient and oxygen deprivation. Importantly, proline-derived reactive oxygen species served as a driving signal for reprogramming. This model has been applied by others to metabolic regulation for the insulin-prosurvival axis, induction of adipose triglyceride lipase for lipid metabolism and regulation of embryonic stem cell development. Of special interest, modulatory proteins such as parkinson protein 7 and oral cancer overexpressed 1 interact with pyrroline-5-carboxylate reductase, a critical component of the proline regulatory axis. Although the interconvertibility of proline and glutamine has been long established, recent findings showed that the proto-oncogene, cellular myelocytomatosis oncogene, upregulates glutamine utilization (glutaminase) and routes glutamate to proline biosynthesis (pyrroline-5-carboxylate synthase, pyrroline-5-carboxylate reductases). Additionally, collagen, which contains large amounts of proline, may be metabolized to serve as a reservoir for proline. This metabolic relationship as well as the new regulatory targets of proline metabolism invites an elucidation of the differential effects of these nonessential amino acids and their production, storage and mobilization. SummaryMechanisms by which the proline regulatory axis modulates the cancer phenotype are being revealed. Proline can be synthesized from glutamine as well as derived from collagen degradation. The metabolism of proline serves as a source of energy during stress, provides signaling reactive oxygen species for epigenetic reprogramming and regulates redox homeostasis.
Assessment of Serum Proteomics to Detect Large Colon Adenomas

A noninvasive blood test that could reliably detect early colorectal cancer or large adenomas would provide an important advance in colon cancer screening. The purpose of this study was to determine whether a serum proteomics assay could discriminate between persons with and without a large (≥1 cm) colon adenoma. To avoid problems of “bias” that have affected many studies about molecular markers for diagnosis, specimens were obtained from a previously conducted study of colorectal cancer etiology in which bloods had been collected before the presence or absence of neoplasm had been determined by colonoscopy, helping to assure that biases related to differences in sample collection and handling would be avoided. Mass spectra of 65 unblinded serum samples were acquired using a nanoelectrospray ionization source on a QSTAR-XL mass spectrometer. Classification patterns were developed using the ProteomeQuest® algorithm, performing measurements twice on each specimen, and then applied to a blinded validation set of 70 specimens. After removing 33 specimens that had discordant results, the “test group” comprised 37 specimens that had never been used in training. Although in the primary analysis, no discrimination was found, a single post hoc analysis, done after hemolyzed specimens had been removed, showed a sensitivity of 78%, a specificity of 53%, and an accuracy of 63% (95% confidence interval, 53-72%). The results of this study, although preliminary, suggest that further study of serum proteomics, in a larger number of appropriate specimens, could be useful. They also highlight the importance of understanding sources of “noise” and “bias” in studies of proteomics assays. (Cancer Epidemiol Biomarkers Prev 2008;17(8):2188–93)