Miracle-dz/UniFAR-FTUs huggingface dataset:
The National Riparian Core Protocol: A riparian vegetation monitoring protocol for wadeable streams of the conterminous United States

Riparian areas are hotspots of biological diversity that may serve as high quality habitat for fish and wildlife. The National Riparian Core Protocol (NRCP) provides tools and methods to assist natural resource professionals in sampling riparian vegetation and physical characteristics along wadeable streams. Guidance is provided for collecting basic information on riparian vegetation composition and physical structure in fluvial riparian ecosystems. The NRCP provides a foundation to assess the characteristics and condition of channels and riparian vegetation at a single point in time or in response to changes in landand water-use activities, including restoration, or natural processes through time.
Practice variation across consent templates for biobank research. a survey of German biobanks

Introduction: Informed, voluntary, and valid consent from biomaterial donors is a precondition for biobank research. Valid consent protects donors’ rights and helps maintain public trust in biobank research. Harmonization of consent procedures in biobank research is needed, because of the widely shared vision on national and international networking of biobanks including data and sample sharing. So far, no study has assessed and compared the content of current consent forms especially for biobank research. The objective of this study was to perform a content analysis of consent forms in German biobanks. Methods: Based on ten guidelines for biomedical research, we developed an assessment matrix with 41 content issues that are potentially relevant for consent forms in biobank research. This assessment matrix was applied in a thematic text analysis to 30 consent documents of German biobanks identified via the German Biobank Registry in July 2012. Results: Coverage of the 41 items in the assessed consent forms varied widely. For example, the items “Right to withdraw consent (without disadvantage),” “Policy for genetic information/consent to genetic analyzes” and “International cooperation/transborder use” were addressed in 97, 40, and 23% of all 30 consent forms respectively. The number of items covered by a single consent form ranged from 9 to 36 (22–88% out of 41 items). Discussion: Our findings serve as a starting point to reflect upon the spectrum of consent issues that must be addressed in biobank research. The findings show that the majority of consent forms for German biobanks, if not all, should be improved and harmonized to better support an informed and balanced choice of potential donors and to facilitate networking of biobanks. Best practice models for consent forms in biobank research should be developed and biobank operators need to be more aware of relevant consent issues.
Cognitive control deficit in patients with first-episode schizophrenia is associated with complex deviations of early brain development

Background Several clinical and radiological markers of early neurodevelopmental deviations have been independently associated with cognitive impairment in patients with schizophrenia. The aim of our study was to test the cumulative and/or interactive effects of these early neurodevelopmental factors on cognitive control (CC) deficit, a core feature of schizophrenia. Methods We recruited patients with first-episode schizophrenia-spectrum disorders, who underwent structural MRI. We evaluated CC efficiency using the Trail Making Test (TMT). Several markers of early brain development were measured: neurological soft signs (NSS), handedness, sulcal pattern of the anterior cingulate cortex (ACC) and ventricle enlargement. Results We included 41 patients with schizophrenia in our analysis, which revealed a main effect of ACC morphology (p = 0.041) as well as interactions between NSS and ACC morphology (p = 0.005), between NSS and handedness (p = 0.044) and between ACC morphology and cerebrospinal fluid (CSF) volume (p = 0.005) on CC measured using the TMT-B score – the TMT-A score. Limitations No 3- or 4-way interactions were detected between the 4 neurodevelopmental factors. The sample size was clearly adapted to detect main effects and 2-way interactions, but may have limited the statistical power to investigate higher-order interactions. The effects of treatment and illness duration were limited as the study design involved only patients with first-episode psychosis. Conclusion To our knowledge, our study provides the first evidence of cumulative and interactive effects of different neurodevelopmental markers on CC efficiency in patients with schizophrenia. Such findings, in line with the neurodevelopmental model of schizophrenia, support the notion that CC impairments in patients with schizophrenia may be the final common pathway of several early neurodevelopmental mechanisms.
Load latency tolerance in dynamically scheduled processors

This paper provides quantitative measurements of load latency tolerance in a dynamically scheduled processor. To determine the latency tolerance of each memory load operation, our simulations use flexible load completion policies instead of a fixed memory hierarchy that dictates the latency. Although our policies delay load completion as long as possible, they produce performance (instructions committed per cycle (IPC)) comparable to an ideal memory system where all loads complete in one cycle. Our measurements reveal that to produce IPC values within 8% of the ideal memory system, between 1% and 62% of loads need to be satisfied within a single cycle and that up to 84% can be satisfied in as many as 32 cycles, depending on the benchmark and processor configuration. Load latency tolerance is largely determined by whether an unpredictable branch is in the load's data dependence graph and the depth of the dependence graph. Our results also show that up to 36% of all loads miss in the level one cache yet have latency demands lower than second level cache access times. We also show that up to 37% of loads hit in the level one cache even though they possess enough latency tolerance to be satisfied by lower levels of the memory hierarchy.
Neuropsychological profile of autism and the broad autism phenotype.

CONTEXT Multiple articles describe a constellation of language, personality, and social-behavioral features present in relatives that mirror the symptom domains of autism, but are much milder in expression. Studies of this broad autism phenotype (BAP) may provide a potentially important complementary approach for detecting the genes causing autism and defining associated neural circuitry by identifying more refined phenotypes that can be measured quantitatively in both affected and unaffected individuals and that are tied to functioning in particular regions of the brain. OBJECTIVE To gain insight into neuropsychological features that index genetic liability to autism. DESIGN Case-control study. SETTING The general community. PARTICIPANTS Thirty-eight high-functioning individuals with autism and parents of autistic individuals, both with and without the BAP (n = 83), as well as control individuals. MAIN OUTCOME MEASURES A comprehensive battery of neuropsychological tasks assessing social cognition, executive function, and global vs local processing strategies (central coherence). RESULTS Both individuals with autism and parents with the BAP differed from controls on measures of social cognition, with performance in the other 2 domains being more similar to controls. CONCLUSIONS Data suggest that the social cognitive domain may be an important target for linking phenotype to cognitive process to brain structure in autism and may ultimately provide insight into the genes involved in autism.
Transfer Learning of Hierarchical Task-Network Planning Methods in a Real-Time Strategy Game

We describe a new integrated and automated AI planning and learning architecture, called Learn2SHOP. Learn2SHOP departs significantly from the previous works on AI planning and learning in that its modular architecture integrates Hierarchical Task Network (HTN) planning, concept learning, and computer simulations. Using simulations during the planning and learning process enables the system to get information about the outcomes of the actions. We have implemented Learn2SHOP and tested it on a transfer-learning task. The objective of transfer learning is transferring knowledge and skills learned from a wide variety of previous situations to the current, and likely different, previously unencountered problems(s). The experiments with Learn2SHOP have demonstrated the advantages of integrating planning, learning, and simulation in a real-time strategy game engine.
How hard is my MDP?" The distribution-norm to the rescue"

In Reinforcement Learning (RL), state-of-the-art algorithms require a large number of samples per state-action pair to estimate the transition kernel p. In many problems, a good approximation of p is not needed. For instance, if from one state-action pair (s, a), one can only transit to states with the same value, learning p(· |s, a) accurately is irrelevant (only its support matters). This paper aims at capturing such behavior by defining a novel hardness measure for Markov Decision Processes (MDPs) based on what we call the distribution-norm. The distribution-norm w.r. t. a measure v is defined on zero v-mean functions f by the standard variation of f with respect to v. We first provide a concentration inequality for the dual of the distribution-norm. This allows us to replace the problem-free, loose ‖ · ‖1 concentration inequalities used in most previous analysis of RL algorithms, with a tighter problem-dependent hardness measure. We then show that several common RL benchmarks have low hardness when measured using the new norm. The distribution-norm captures finer properties than the number of states or the diameter and can be used to assess the difficulty of MDPs.
Dose Reduction in Abdominal Computed Tomography: Intraindividual Comparison of Image Quality of Full-Dose Standard and Half-Dose Iterative Reconstructions With Dual-Source Computed Tomography

Objectives:We sought to evaluate the image quality of iterative reconstruction in image space (IRIS) in half-dose (HD) datasets compared with full-dose (FD) and HD filtered back projection (FBP) reconstruction in abdominal computed tomography (CT). Materials and Methods:To acquire data with FD and HD simultaneously, contrast-enhanced abdominal CT was performed with a dual-source CT system, both tubes operating at 120 kV, 100 ref.mAs, and pitch 0.8. Three different image datasets were reconstructed from the raw data: Standard FD images applying FBP which served as reference, HD images applying FBP and HD images applying IRIS. For the HD data sets, only data from 1 tube detector-system was used. Quantitative image quality analysis was performed by measuring image noise in tissue and air. Qualitative image quality was evaluated according to the European Guidelines on Quality criteria for CT. Additional assessment of artifacts, lesion conspicuity, and edge sharpness was performed. Results:Image noise in soft tissue was substantially decreased in HD-IRIS (−3.4 HU, −22%) and increased in HD-FBP (+6.2 HU, +39%) images when compared with the reference (mean noise, 15.9 HU). No significant differences between the FD-FBP and HD-IRIS images were found for the visually sharp anatomic reproduction, overall diagnostic acceptability (P = 0.923), lesion conspicuity (P = 0.592), and edge sharpness (P = 0.589), while HD-FBP was rated inferior. Streak artifacts and beam hardening was significantly more prominent in HD-FBP while HD-IRIS images exhibited a slightly different noise pattern. Conclusions:Direct intrapatient comparison of standard FD body protocols and HD-IRIS reconstruction suggest that the latest iterative reconstruction algorithms allow for approximately 50% dose reduction without deterioration of the high image quality necessary for confident diagnosis.
Protecting and evaluating genomic privacy in medical tests and personalized medicine

In this paper, we propose privacy-enhancing technologies for medical tests and personalized medicine methods that use patients' genomic data. Focusing on genetic disease-susceptibility tests, we develop a new architecture (between the patient and the medical unit) and propose a "privacy-preserving disease susceptibility test" (PDS) by using homomorphic encryption and proxy re-encryption. Assuming the whole genome sequencing to be done by a certified institution, we propose to store patients' genomic data encrypted by their public keys at a "storage and processing unit" (SPU). Our proposed solution lets the medical unit retrieve the encrypted genomic data from the SPU and process it for medical tests and personalized medicine methods, while preserving the privacy of patients' genomic data. We also quantify the genomic privacy of a patient (from the medical unit's point of view) and show how a patient's genomic privacy decreases with the genetic tests he undergoes due to (i) the nature of the genetic test, and (ii) the characteristics of the genomic data. Furthermore, we show how basic policies and obfuscation methods help to keep the genomic privacy of a patient at a high level. We also implement and show, via a complexity analysis, the practicality of PDS.
Robust Fuzzy Extractors and Helper Data Manipulation Attacks Revisited: Theory versus Practice

Fuzzy extractors have been proposed in 2004 by Dodis et al. as a secure way to generate cryptographic keys from noisy sources. In recent years, fuzzy extractors have become an important building block in hardware security due to their use in secure key generation based on Physical Unclonable Functions (PUFs). Fuzzy extractors are provably secure against passive attackers. A year later Boyen et al. introduced robust fuzzy extractors which are also provably secure against active attackers, i.e., attackers that can manipulate the helper data. In this paper we show that the original provable secure robust fuzzy extractor construction by Boyen et al. actually does not fulfill the error-correction requirements for practical PUF applications. The fuzzy extractors proposed for PUF-based key generation on the other hand that fulfill the error-correction requirements cannot be extended to such robust fuzzy extractors, due to a strict bound $t$t on the number of correctable errors. While it is therefore tempting to simply ignore this strict bound, we present novel helper data manipulation attacks on fuzzy extractors that also work if a “robust fuzzy extractor-like” construction without this strict bound is used. Hence, this paper can be seen as a call for action to revisit this seemingly solved problem of building robust fuzzy extractors. The new focus should be on building more efficient solutions in terms of error-correction capability, even if this might come at the costs of a proof in a weaker security model.
Part-based pedestrian detection using grammar model and ABM-HoG features

To handle the pedestrian appearance and pose variations in complex traffic environments, we present one part-based pedestrian detection approach using a stochastic grammar model in this paper. The And-Or graph model is introduced to represent the human body as an assembly of compositional and reconfigurable parts. Thus, the task of detection is converted into the human parsing problem, which is a Bayesian inference process. We model the appearance of pedestrian parts in a rich feature representation. This appearance model enhances the Histogram of Gradients (HoG) map with Active Basis Model (ABM), which is a sparse deformable template depicting salient structures of objects. Then, geometry constraints among parts are described by Gaussian distributions. Finally, the bottom-up parsing inference is conducted by aggregating scores to get the pedestrian detection responses. In experiments, we show the superiority of our appearance model, as well as the reliable pedestrian detection results of our approach in complex traffic scenes.
peer file-sharing using social-network sites

Social networking sites and peer-to-peer systems are two concepts that are being applied in our daily life. This paper combines the strong characteristics of these two concepts: using the social-network sites to provide access control to available data and the peer-to-peer system to distribute this available data. In particular, this paper combines the fine-grained access control that social-network sites offer and efficient file-sharing throughput of peer-topeer systems. An architecture is proposed that uses and enhances the features provided by the Facebook social network and by the OneSwarm file-sharing system.
Geologic Framework and Hydrogeologic Characteristics of the Edwards Aquifer Recharge Zone, Bexar County, Texas

Abstract In Bexar County, residential and commercial development on the Edwards aquifer recharge zone is increasing. The aquifer possibly can be contaminated by spills, leakage of hazardous materials, or runoff from the rapidly developing urban areas that surround, or are built on, the intensely faulted and fractured, karstic limestone outcrops characteristic of the recharge zone. Furthermore, some of the hydrogeologic subdivisions that compose the Edwards aquifer have greater effective porosity than others. The areas where the most porous subdivisions crop out might provide efficient avenues for contaminants to enter the aquifer. The Edwards aquifer recharge zone has relatively large permeability resulting, in part, from the development or redistribution of secondary porosity. Lithology, stratigraphy, diagenesis, and karstification account for the effective porosity and permeability in the Edwards aquifer outcrop. Karst features that greatly enhance effective porosity in the outcrop area include sinkholes and caves. Hydrogeologic subdivision VI, the Kirschberg evaporite member, appears to be the most porous and permeable subdivision within the Kainer Formation. Hydrogeologic subdivision III, the leached and collapsed members, undivided, is the most porous and permeable subdivision within the Person Formation. Hydrogeologic subdivision II, the cyclic and marine members, undivided, is moderately permeable, with both fabric- and not-fabric-selective porosity. The faults in northern Bexar County are part of the Balcones fault zone. Although most of the faults in this area trend northeast, a smaller set of cross-faults trend northwest. Generally, the faults are en echelon and normal, with the downthrown blocks typically toward the coast.
Targeting Platelet GPVI Plus rt-PA Administration but Not α2β1-Mediated Collagen Binding Protects against Ischemic Brain Damage in Mice

Platelet collagen interactions at sites of vascular injuries predominantly involve glycoprotein VI (GPVI) and the integrin α2β1. Both proteins are primarily expressed on platelets and megakaryocytes whereas GPVI expression is also shown on endothelial and integrin α2β1 expression on epithelial cells. We recently showed that depletion of GPVI improves stroke outcome without increasing the risk of cerebral hemorrhage. Genetic variants associated with higher platelet surface integrin α2 (ITGA2) receptor levels have frequently been found to correlate with an increased risk of ischemic stroke in patients. However until now, no preclinical stroke study has addressed whether platelet integrin α2β1 contributes to the pathophysiology of ischemia/reperfusion (I/R) injury. Focal cerebral ischemia was induced in C57BL/6 and Itga2−/− mice by a 60 min transient middle cerebral artery occlusion (tMCAO). Additionally, wild-type animals were pretreated with anti-GPVI antibody (JAQ1) or Fab fragments of a function blocking antibody against integrin α2β1 (LEN/B). In anti-GPVI treated animals, intravenous (IV) recombinant tissue plasminogen activator (rt-PA) treatment was applied immediately prior to reperfusion. Stroke outcome, including infarct size and neurological scoring was determined on day 1 after tMCAO. We demonstrate that targeting the integrin α2β1 (pharmacologic; genetic) did neither reduce stroke size nor improve functional outcome on day 1 after tMCAO. In contrast, depletion of platelet GPVI prior to stroke was safe and effective, even when combined with rt-PA treatment. Our results underscore that GPVI, but not ITGA2, is a promising and safe target in the setting of ischemic stroke.
Efficient resource allocation in clustered wireless mesh networks

Due to the requisite of multi-channel communications for high-speed data transmissions, power allocation for opportunistically exploiting fading wireless channels, and packet scheduling for quality-of-service provisioning, joint power-frequency-time resource allocation is indispensable. In this paper, we propose a low-complexity intra-cluster resource allocation algorithm, taking power allocation, subcarrier allocation, and packet scheduling into consideration. Numerical results demonstrate that our algorithm is close to optimal, and that our optimality-driven resource allocation algorithm outperforms a greedy algorithm, achieving higher resource utilization and better performance compromise among throughput, packet dropping rate, and packet delay.
On the MIMO interference channel

We propose an iterative algorithm to design optimal linear transmitters and receivers in a K-user frequency-flat MIMO Interference Channel (MIMO IFC) with full channel state information (CSI). The transmitters and receivers are optimized to maximize the Weighted Sum Rate (WSR) of the MIMO IFC. Maximization of WSR is desirable since it allows the system to cover all the rate tuples on the Pareto-optimal rate region boundary for a given MIMO IFC. The proposed algorithm is rooted in a recent result [1] showing a correspondence between local optima of the Minimum Weighted Sum Mean Squared Error (MWSMSE) and Maximum Weighted Sum Rate (MWSR) objective functions for the MIMO Broadcast Channel (BC). This connection between the MWSR and MWSMSE is shown to hold true also in the MIMO IFC and is exploited to design an alternating minimization algorithm for MIMO IFC that maximizes the WSR. The MWSMSE-MWSR connection also allows to solve the transmit filter design subproblem in the alternating algorithm by invoking a heuristic solution first proposed in [2],[3]. Another contribution of this paper is to propose an extension of [4] to MIMO problems, following the philosophy of [1] in part. This path is shown to lead in fact to the same iterative algorithm, showing the optimality of the heuristic of [2],[3] when applied in the context of the alternating transmitter-receiver optimization approach of [1].
Generating Varied Narrative Probability Exercises

This paper presents Genpex, a system for automatic generation of narrative probability exercises. Generation of exercises in Genpex is done in two steps. First, the system creates a specification of a solvable probability problem, based on input from the user (a researcher or test developer) who selects a specific question type and a narrative context for the problem. Then, a text expressing the probability problem is generated. The user can tune the generated text by setting the values of some linguistic variation parameters. By varying the mathematical content of the exercise, its narrative context and the linguistic parameter settings, many different exercises can be produced. Here we focus on the natural language generation part of Genpex. After describing how the system works, we briefly present our first evaluation results, and discuss some aspects requiring further investigation.