Miracle-dz/UniFAR-FTUs huggingface dataset:
A Framework for Collaborative Curation of Neuroscientific Literature

Large models of complex neuronal circuits require specifying numerous parameters, with values that often need to be extracted from the literature, a tedious and error-prone process. To help establishing shareable curated corpora of annotations, we have developed a literature curation framework comprising an annotation format, a Python API (NeuroAnnotation Toolbox; NAT), and a user-friendly graphical interface (NeuroCurator). This framework allows the systematic annotation of relevant statements and model parameters. The context of the annotated content is made explicit in a standard way by associating it with ontological terms (e.g., species, cell types, brain regions). The exact position of the annotated content within a document is specified by the starting character of the annotated text, or the number of the figure, the equation, or the table, depending on the context. Alternatively, the provenance of parameters can also be specified by bounding boxes. Parameter types are linked to curated experimental values so that they can be systematically integrated into models. We demonstrate the use of this approach by releasing a corpus describing different modeling parameters associated with thalamo-cortical circuitry. The proposed framework supports a rigorous management of large sets of parameters, solving common difficulties in their traceability. Further, it allows easier classification of literature information and more efficient and systematic integration of such information into models and analyses.
Is scientific excellence a probabilistic consequence of quantity ? On the relationship between productivity , impact , and excellence among early career researchers in mathematics

Bibliometric indicators are increasingly used in science policy to identify and stimulate research excellence by allocating resources on the basis of publication and citation statistics (Abramo, Cicero, & D’angelo 2014). The most commonly used indicators for identifying scientific excellence are citation based indicators of highly cited papers (e.g., top k %; Bornmann 2014; Zitt, Ramanana-Rahary, & Bassecoulard 2005). At the level of individual researchers this would suggest that an excellent researcher is one that produces highly cited articles (Abramo, Cicero, & D’angelo 2014). The use of citation based indicators as decision support tools to concentrate resources at the individual level is based on the assumption that the publication track record of a researcher can be used to predict whether or not that researcher will produce excellent research in the future, i.e., that there is continuity between the researcher’s past and future achievements in science (Danell 2011). However, the information value of citation based measures in the context of selecting for excellence is questioned by the so called constant-probability-of-success model proposed by Simonton (1985; 1997; 2003).
Iterative MIMO Effective SNR Mapping for ML Decoder

A new performance abstraction method for the Maximum Likelihood Decoder (MLD) in the Multiple-Inputs Multiple-Outputs (MIMO) channel is presented. The method is based on a model of the iterative equalize and de-map decoder for MIMO channel and abstracts the performance of the MIMO link into a set of effective Signal-to-Noise power Ratio (SNR) values corresponding to the different streams. The proposed Iterative MIMO Effective SNR (IMES) approach is general and allows for the use of different modulation constellations and independent channel encoding on the MIMO streams. The low complexity IMES technique can be applied to different MIMO configurations and can be combined with existing approaches -such as Exponential Effective SNR Mapping (EESM) and Mean Mutual Information per Bit (MMIB) - for link performance abstraction of MIMO OFDM systems. Performance results show that the proposed method delivers accurate performance abstraction across configurations with different numbers of transmit antennas and input constellation modulation orders.
Particle-associated organic compounds and symptoms in myocardial infarction survivors

Context: The aerosol components responsible for the adverse health effects of the exposure to particulate matter (PM) have not been conclusively identified, and there is especially little information on the role of particulate organic compounds (POC). Objective: This study evaluated the role of PM and POC with regard to daily symptoms. Methods: One hundred and fifty-three myocardial infarction survivors from Augsburg, Germany, recorded daily occurrence of different symptoms in winter 2003/2004. Ambient concentrations of PM with a diameter <2.5 μm (PM2.5), particle number concentration (PNC), PM2.5-bound hopanes, and polycyclic aromatic hydrocarbons (PAH) were quantified. Data were analyzed using generalized estimating equations adjusting for meteorological and other time-variant confounders. Results: The odds for avoidance of physically demanding activities due to heart problems increased immediately associated with most POC measures (e.g. 5% per 1.08 ng/m3 increase in benzo[a]pyrene, 95%-confidence interval (CI):1–9%) and tended to a delayed decrease. After a 2-day delayed decrease associated with hopanes, the odds for shortness of breath increased consistently after 3 days with almost all POC measures (e.g. 4% per 0.21 ng/m3 increase in 17α(H), 21β(H)-hopane, CI: 1–8%). The odds for heart palpitations marginally increased immediately in association with PNC (8% per 8146 cm−3 increase in PNC, CI: 0–16%). Conclusions: The study showed an association between PM, particle-bound POC, and daily symptoms. The organic compounds may be causally related with cardiovascular health or act rather as indicators for traffic- and combustion-related particles.
Loss of Cardiolipin Leads to Perturbation of Mitochondrial and Cellular Iron Homeostasis*

Background: Cardiolipin (CL) deficiency causes multiple defects affecting mitochondrial bioenergetics. Results: CL deficiency leads to defective mitochondrial Fe-S biogenesis, causing decreased activity of several mitochondrial and cytosolic Fe-S proteins and perturbation of iron homeostasis. Conclusion: CL is an important regulator of mitochondrial and cellular iron homeostasis. Significance: Mitochondrial iron homeostasis may be an important physiological modifier that contributes to the clinical phenotypes observed in Barth syndrome patients. Cardiolipin (CL) is the signature phospholipid of mitochondrial membranes, where it is synthesized locally and plays a critical role in mitochondrial bioenergetic functions. The importance of CL in human health is underscored by the observation that perturbation of CL biosynthesis causes the severe genetic disorder Barth syndrome. To fully understand the cellular response to the loss of CL, we carried out genome-wide expression profiling of the yeast CL mutant crd1Δ. Our results show that the loss of CL in this mutant leads to increased expression of iron uptake genes accompanied by elevated levels of mitochondrial iron and increased sensitivity to iron and hydrogen peroxide. Previous studies have shown that increased mitochondrial iron levels result from perturbations in iron-sulfur (Fe-S) cluster biogenesis. Consistent with an Fe-S defect, deletion of ISU1, one of two ISU genes that encode the mitochondrial Fe-S scaffolding protein essential for the synthesis of Fe-S clusters, led to synthetic growth defects with the crd1Δ mutant. We further show that crd1Δ cells have reduced activities of mitochondrial Fe-S enzymes (aconitase, succinate dehydrogenase, and ubiquinol-cytochrome c oxidoreductase), as well as cytosolic Fe-S enzymes (sulfite reductase and isopropylmalate isomerase). Increased expression of ATM1 or YAP1 did not rescue the Fe-S defects in crd1Δ. These findings show for the first time that CL is required for Fe-S biogenesis to maintain mitochondrial and cellular iron homeostasis.
Characterization and oil-degrading activity of heavy oil-degrading bacteria isolated from the sea water of oil-polluted Bisan Seto and oil-unpolluted Hibiki Nada [Japan]

The flora of heavy oil-degrading bacteria isolated from water samples collected in oil-polluted Bisan Seto and oil-unpolluted Hibiki Nada was investigated. The oil-degrading activity of the isolated strains was also measured. It was observed that coryneforms were exclusively dominant among oil-degrading isolates in oil-polluted Bisan Seto. In oil-unpolluted Hibiki Nada, coryne forms and Pseudomonas were isolated in the same ratio. Oil-degrading activity of coryneforms was much higher than that of Pseudomonas, regardless of where they were isolated. From these results, it was suggested that coryneforms play an important role in the biodegradation of oil in oil polluted Biasn Seto. When the average oil-degrading activity of the strains isolated from Bisan Seto and that from Hibiki Nada was compared, the former (21.6%) was significantly higher than the latter (14.1%). It was suggested that the flora and oil-degrading activity of oil-degrading bacteria were sensitive indicators of oil-pollution than other factors previously examined (i.e. numbers of oil degrading bacteria, the ratio of the degraders to the total heterotrophs).
Object Oriented Software Effort Estimate with Adaptive Neuro Fuzzy use Case Size Point (ANFUSP)

Use case size point (USP) method has been proposed to estimate object oriented software development effort in early phase of software project and used in a lot of software organizations. Intuitively, USP is measured by counting the number of actors, preconditions, post conditions, scenarios included in use case models. In this paper have presented a Adaptive fuzzy Neural Network model to estimate the effort of object oriented software using Use Case size Point approach. In our proposed system adaptive neural network fuzzy use case size point has less error and system worked more accurate and appropriative than prior methods.
Subpopulations of Neurons in Visual Area V2 Perform Differentiation and Integration Operations in Space and Time

The interconnected areas of the visual system work together to find object boundaries in visual scenes. Primary visual cortex (V1) mainly extracts oriented luminance boundaries, while secondary visual cortex (V2) also detects boundaries defined by differences in texture. How the outputs of V1 neurons are combined to allow for the extraction of these more complex boundaries in V2 is as of yet unclear. To address this question, we probed the processing of orientation signals in single neurons in V1 and V2, focusing on response dynamics of neurons to patches of oriented gratings and to combinations of gratings in neighboring patches and sequential time frames. We found two kinds of response dynamics in V2, both of which were different from those of V1 neurons. While V1 neurons in general preferred one orientation, one subpopulation of V2 neurons (“transient”) showed a temporally dynamic preference, resulting in a preference for changes in orientation. The second subpopulation of V2 neurons (“sustained”) responded similarly to V1 neurons, but with a delay. The dynamics of nonlinear responses to combinations of gratings reinforced these distinctions: the dynamics enhanced the preference of V1 neurons for continuous orientations and the preference of V2 transient neurons for discontinuous ones. We propose that transient neurons in V2 perform a differentiation operation on the V1 input, both spatially and temporally, while the sustained neurons perform an integration operation. We show that a simple feedforward network with delayed inhibition can account for the temporal but not for the spatial differentiation operation.
Structure of intact Thermus thermophilus V-ATPase by cryo-EM reveals organization of the membrane-bound VO motor

The eubacterium Thermus thermophilus uses a macromolecular assembly closely related to eukaryotic V-ATPase to produce its supply of ATP. This simplified V-ATPase offers several advantages over eukaryotic V-ATPases for structural analysis and investigation of the mechanism of the enzyme. Here we report the structure of the complex at ∼16 Å resolution as determined by single particle electron cryomicroscopy (cryo-EM). The resolution of the map and our use of cryo-EM, rather than negative stain EM, reveals detailed information about the internal organization of the assembly. We could separate the map into segments corresponding to subunits A and B, the threefold pseudosymmetric C-subunit, a central rotor consisting of subunits D and F, the L-ring, the stator subcomplex consisting of subunits I, E, and G, and a micelle of bound detergent. The architecture of the VO region shows a remarkably small area of contact between the I-subunit and the ring of L-subunits and is consistent with a two half-channel model for proton translocation. The arrangement of structural elements in VO gives insight into the mechanism of torque generation from proton translocation.
Wide-coverage parsing of speech transcripts

This paper discusses the performance difference of wide-coverage parsers on small-domain speech transcripts. Two parsers (C&C CCG and RASP) are tested on the speech transcripts of two different domains (parent-child language, and picture descriptions). The performance difference between the domain-independent parsers and two domain-trained parsers (MSTParser and MEGRASP) is substantial, with a difference of at least 30 percent point in accuracy. Despite this gap, some of the grammatical relations can still be recovered reliably.
Stability margin via reflection vectors

A new stability margin for discrete-time systems is proposed in the system characteristic polynomial coefficient space making use of, so-called, reflection vectors of monic Schur polynomials. Reflection vector margins give the distance to the stability boundary in directions of In reflection vectors of an n-th degree polynomial. The relations between the reflection vectors and its roots on the unit circle are obtained. An iterative procedure for stability radius determination is proposed.
What is a psychological intervention? A metareview and practical proposal

Objective: What do we mean by a ‘psychological intervention’ in the context of cancer care? It is critical to know what treatments are included under this term, if data from diverse treatment trials are to be summarized in order to inform clinical practice. We, therefore, aimed to determine how the term ‘psychological intervention’ has been defined and used to group and compare interventions in reviews of cancer care.
No 04-03 Industrial Clustering and the Returns to Inventive Activity : Canadian Biotechnology Firms , 1991-2000 by

We examine how industrial clustering affects biotechnology firms’ innovativeness, contrasting similar firms not located in clusters or located in clusters that are or are not focused on the firm’s technological specialization. Using detailed firm level data, we find clustered firms are eight times more innovative than geographically remote firms, with largest effects for firms located in clusters strong in their own specialization. For firms located in a cluster strong in their specialization we also find that R&D productivity is enhanced by a firm’s own R&D alliances and also by the R&D alliances of other colocated firms.
Population ecology of nitrifying bacteria.

INTRODUCTION 309 DIVERSITY AND DISTRIBUTION 3 10 Generic Diversity 310 Immunologic Diversity and Distribution 3 1 2 METHODS FOR ESTIMATING NITRIFIER POPULATIONS . 313 MPN Technique 313 FA Counting Techniques 3 14 Activity Measurements and Counting Efficiencies . 3 1 5 Ecological Studies and MPN Counts 3 1 8 Heterotrophic nitrification 3 1 8 Inhibition o f nitrification b y climax ecosystems . 3 1 9 Comparison o f the Methods 320 FACTORS THAT REGULATE POPULATION SIZE 321 Substrates and Products of Nitrification 321 Sources of substrate 321 Properties of substrates and products . 321 Ammonium as a Limiting Substrate 322 Growth Yields in Soils 324 Population Regulation when Ammonium is not Limiting 325 Conditions Adverse to Population Growth and Maintenance . : 327 Growth 0/ Nitrifiers 328 Diff erential Growth 0/ Nitrijiers and the Accumulation 0/ Nitrite 329 CONCLUDING REMARKS 3 3 1
Community-based assessments of change, contributions of Inuvialuit knowledge to understanding climate change in the Canadian Arctic

Inuit and huvialuit in the Canadian Arctic possess a substantial body of knowledge and expertise related to cümate and climate change. The weather. and the relationship between weather and other environmental phenomena, is closely monitored in northem communi ties. Variabiii ty and fluctuation are expected elements of local environmental patterns and processes. However, in the past 10 years cornrnunities have begun to experirnce changes that they consider to be beyond the range of normal variability. Community assessments of change are based on cumulative knowledge of local trends, patterns and processes. derived from generations of experience. The Arctic is considered by many to be the "canary" of climate change; an early warning sign of the impacts of change. Thus, high latitude regions have becorne a focal point for climate change research. However, there is significant difficulty associated with discerning regionai differences and predicting impacts at the local scale. CLimate science in northem regions is often cornplicated by insufficient observational data, seasonal limitations and a lack of badine data against which to compare change. An emerging theme in climate research is bridging the gap between Western science and Inuit knowledge of climate change to better understand Arctic climate change. This thesis is encouragement for this theme. Based in part on the collaborative research project Inuit Observations of Climare Change (1999-20) in Sachs Harbour, Western Canadian Arctic, 1 descnbe how local, land-based expertise and community-based assessments cm provide observations, predictions and explanations of climate change at scales and in contexts currently underrepresented in climate change research. Firsthand experience working with local experts and scientists is used as a basis for a conceptual frarnework that explains how to find cornmon ground between Inuvialuit traditional knowledge and Western science. This framework includes five areas of convergence in which traditionai knowledge cm complement scientific approches to understanding climate change in the Canadian Arctic. These areas are: the contributions of traditional knowledge (i) as local scale expertise; (ii) as a source of climate history and baseline data; (iii) in formulating research questions and hypotheses; (iv) as insight into impacts and adaptation in Arctic communities; and (v) for long term. communitybased monitoring.
Implementing global memory management in a workstation cluster

Advances in network and processor technology have greatly changed the communication and computational power of local-area workstation clusters. However, operating systems still treat workstation clusters as a collection of loosely-connected processors, where each workstation acts as an autonomous and independent agent. This operating system structure makes it difficult to exploit the characteristics of current clusters, such as low-latency communication, huge primary memories, and high-speed processors, in order to improve the performance of cluster applications. This paper describes the design and implementation of global memory management in a workstation cluster. Our objective is to use a single, unified, but distributed memory management algorithm at the lowest level of the operating system. By managing memory globally at this level, all system- and higher-level software, including VM, file systems, transaction systems, and user applications, can benefit from available cluster memory. We have implemented our algorithm in the OSF/1 operating system running on an ATM-connected cluster of DEC Alpha workstations. Our measurements show that on a suite of memory-intensive programs, our system improves performance by a factor of 1.5 to 3.5. We also show that our algorithm has a performance advantage over others that have been proposed in the past.
Secrecy capacities of compound quantum wiretap channels and applications

We determine the secrecy capacity of the compound channel with quantumwiretapper and channel state information at the transmitter. Moreover, wederive a lower bound on the secrecy capacity of this channel without channelstate information and determine the secrecy capacity of the compoundclassical-quantum wiretap channel with channel state information at thetransmitter. We use this result to derive a new proof for a lower bound on theentanglement generating capacity of compound quantum channel. We also derive anew proof for the entanglement generating capacity of compound quantum channelwith channel state information at the encoder.
Tisseel's impact on hemostasis for 2–3 and 4–6-level lumbar laminectomies

Background: Tisseel (Baxter International Inc., Westlake Village, CA, USA), a fibrin sealant, was originally devised to strengthen repairs of spinal cerebrospinal fluid (CSF) fistulas. Here, we evaluated how Tisseel correlated with hemostasis (e.g., defined as reduced postoperative drainage, time to drain removal, length of stay (LOS), and postoperative transfusion requirements) in 58 patients undergoing 2–3 vs. 79 patients having 4–6 level lumbar laminectomies. Methods: We assessed how Tisseel correlated with hemostasis in 58 patients undergoing 2–3 level laminectomies/stenosis (with 48 herniated discs and 20 synovial cysts, 1 degenerative spondylolisthesis) vs. 79 having 4–6 level laminectomies/stenosis (with 39 lumbar discs, 45 synovial cysts, and 26 degenerative spondylolisthesis). Results: Following 2–3 level laminectomies, the average drainage on postoperative day 1 was 87.26 cc, and on day 2 was 59.62 cc; most drains were removed and the majority of patients were discharged on postoperative day 2, requiring no transfusions. After 4–6 level decompressions, greater postoperative drainage was observed on postoperative days 1 (e.g., 156.63 cc), and 2 (115.8 cc), and many were continued for 3 (85.7 cc; 44 patients), and 4 postoperative days (93.6: 6 patients) respectively. Drains were typically removed and patients were discharged on postoperative days 3 and 4, with just 6 requiring transfusions. Notably, there were four CSF fistulas for patients undergoing 4–6 level laminectomies; one had a large disc hernation in conjunction with postoperative scare, while three had massive calcified synovial cysts extending to/through the dura. Conclusions: Utilizing Tisseel as a hemostatic allowed us to quantitate hemostasis (the average postoperative drainage, time to drain removal, LOS, and postoperative transfusion requirements) for those undergoing 2–3 level laminectomies vs. 4–6 level procedures with large subsets also exhibiting herniated discs, synovial cysts, and degenerative spondylolisthesis.