Miracle-dz/UniFAR-FTUs huggingface dataset:
Gideon-TS: Efﬁcient Exploration and Labeling of Multivariate Industrial Sensor Data

: Modern digitization in industrial production requires the acquisition of process data that is subsequently used in analysis and optimization scenarios. For this purpose, the use of machine learning methods has become more and more established in recent years. However, training advanced machine learning models from scratch requires a lot of labeled data. The creation of such labeled data is a major challenge for many companies, as the generation process cannot be fully automated and is therefore very time-consuming and expensive. Thus, the need for corresponding software tools to label complex data streams, such as sensor data, is steadily increasing. Existing contributions are not designed for handling large datasets and forms common for industrial applications, and offer little support for the labeling of large data volumes. For this reason, we introduce Gideon-TS — an interactive labeling tool for sensor data that is tailored to the needs of industrial use. Gideon-TS can integrate time series datasets in multiple modalities (univariate, multivariate, samples, with and without timestamp) and remains performant even with large datasets. We also present an approach to semi-automatic labeling that reduces the time needed to label large volumes of data. We evaluated Gideon-TS on an industrial exemplary use case by conducting performance tests and a user study to show that it is suitable for labeling large datasets and signiﬁcantly reduces labeling time compared to traditional labeling methods.
Steroid Hormone Synthesis by Vaccinia Virus Suppresses the Inflammatory Response to Infection

The 3β-hydroxysteroid dehydrogenase (3β-HSD) isoenzymes play a key role in cellular steroid hormone synthesis. Vaccinia virus (VV) also synthesizes steroid hormones with a 3β-HSD enzyme (v3β-HSD) encoded by gene A44L. Here we examined the effects of v3β-HSD in VV disease using wild-type (vA44L), deletion (vΔA44L), and revertant (vA44L-rev) viruses in a murine intranasal model. Loss of A44L was associated with an attenuated phenotype. Early (days 1–3) after infection with vΔA44L or control viruses the only difference observed between groups was the reduced corticosterone level in lungs and plasma of vΔA44L-infected animals. Other parameters examined (body weight, signs of illness, temperature, virus titres, the pulmonary inflammatory infiltrate, and interferon [IFN]-γ levels) were indistinguishable between groups. Subsequently, vΔA44L-infected animals had reduced weight loss and signs of illness, and displayed a vigorous pulmonary inflammatory response. This was characterized by rapid recruitment of CD4+ and CD8+ lymphocytes, enhanced IFN-γ production and augmented cytotoxic T lymphocyte activity. These data suggest that steroid production by v3β-HSD contributes to virus virulence by inhibiting an effective inflammatory response to infection.
Assessing the Effects of Climate Change on Aquatic Invasive Species

Abstract: Different components of global environmental change are typically studied and managed independently, although there is a growing recognition that multiple drivers often interact in complex and nonadditive ways. We present a conceptual framework and empirical review of the interactive effects of climate change and invasive species in freshwater ecosystems. Climate change is expected to result in warmer water temperatures, shorter duration of ice cover, altered streamflow patterns, increased salinization, and increased demand for water storage and conveyance structures. These changes will alter the pathways by which non‐native species enter aquatic systems by expanding fish‐culture facilities and water gardens to new areas and by facilitating the spread of species during floods. Climate change will influence the likelihood of new species becoming established by eliminating cold temperatures or winter hypoxia that currently prevent survival and by increasing the construction of reservoirs that serve as hotspots for invasive species. Climate change will modify the ecological impacts of invasive species by enhancing their competitive and predatory effects on native species and by increasing the virulence of some diseases. As a result of climate change, new prevention and control strategies such as barrier construction or removal efforts may be needed to control invasive species that currently have only moderate effects or that are limited by seasonally unfavorable conditions. Although most researchers focus on how climate change will increase the number and severity of invasions, some invasive coldwater species may be unable to persist under the new climate conditions. Our findings highlight the complex interactions between climate change and invasive species that will influence how aquatic ecosystems and their biota will respond to novel environmental conditions.
Branch-and-Price for the Steiner Tree Problem with Revenues , Budget and Hop Constraints

This thesis deals with the Steiner tree problem with revenues, budget and hop constraints (STPRBH), an NP-hard combinatorial optimization problem with applications in telecommunications network design. An instance of the STPRBH is defined by a connected graph with a dedicated root node, a set of nodes with nonnegative revenues and positive costs assigned to edges. Furthermore, a budgetB ≥ 0 and a hop limitH ∈ N are given. The set of feasible solutions is given by all Steiner trees containing the root node, where every path from the root node to any other node in the tree contains at most H edges. Furthermore, the total edge costs of such a tree must be lower or equal to the given budget B. The goal is to find a feasible solution with maximum revenue, i.e. to maximize the sum of revenues associated with nodes which are part of the solution. Several formulations for the STPRBH based on integer linear programming using exponentially many variables are presented. Furthermore, branch-and-price approaches based on these formulations are introduced that allow for solving instances of the STPRBH to proven optimality. The practical implementations of these branch-and-price approaches do, however, suffer from various problems. Thus, the applicability of various attempts to improve their efficiency like stabilization techniques, different pricing strategies and heuristic methods to generate initial solutions is analyzed. Furthermore, promising methods are correspondingly adapted and applied to the STPRBH. Tests on previously existing benchmark instances show that the presented branch-and-price approaches are competitive with existing exact methods based on branch-and-cut when the hop limit is rather restrictive or if the number of nodes with positive revenue is relatively small. Furthermore, when the budget B does not play a role (i.e. is high enough to pose no restriction), branch-and-price usually outperforms branch-and-cut. It should be noted, however, that this specific variant of the STPRBH is not NP -hard. For instances with a large hop limit or a large number of nodes with positive revenue the proposed branch-and-price approaches are not yet competitive to branch-and-cut. Due to the implemented stabilization and acceleration methods a significant speed-up of branch-and-price has, however, been achieved for these instances too.
Deregressed genomic breeding values from single-step evaluations of test-day traits using all genotype data

Single-step model has become the Golden Standard for routine genetic evaluation in dairy cattle. For various statistical analyses or genomic validation, (daughter) yield deviations or deregressed genomic breeding values may be considered as pseudo-phenotype that are more independent from early genomic prediction. The aims of this study were to assess GEBV deregression methods for cows and bulls, and to validate the deregressed GEBV via a reversibility test. A total of 13.5 million animals with phenotypic records, evaluated with a single-step model using the German genotypic and phenotypic data from April 2023, were considered in the cow GEBV deregression. Likewise, all bulls with daughters and all reference cows were included in the bull GEBV deregression. Both GEBV deregression processes used the same genotype data and pedigree file as the preceding single-step evaluation. Deregressed GEBV of the cows or the bulls were moderately or highly correlated with their GEB, respectively. For the four test-day traits, milk, fat and protein yields and somatic cell scores, the deregressed GEBV seemed to have a lower trend than their original GEBV. Equal GEBV were obtained in a special single-step evaluation using the deregressed GEBV as phenotypic data, in comparison to those GEBV from the original single-step evaluation. We obtained equal GEBV not only for the cows with test-day records and bulls with daughters but nearly equal also for young, genotyped candidates without own phenotypic records. The validation results confirmed that the GEBV deregression was a reversible process and the deregressed GEBV were proven to be correct.
JNK Contributes to Hif-1α Regulation in Hypoxic Neurons

Hypoxia is an established factor of neurodegeneration. Nowadays, attention is directed at understanding how alterations in the expression of stress-related signaling proteins contribute to age dependent neuronal vulnerability to injury. The purpose of this study was to investigate how Hif-1α, a major neuroprotective factor, and JNK signaling, a key pathway in neurodegeneration, relate to hypoxic injury in young (6DIV) and adult (12DIV) neurons. We could show that in young neurons as compared to mature ones, the protective factor Hif-1α is more induced while the stress protein phospho-JNK displays lower basal levels. Indeed, changes in the expression levels of these proteins correlated with increased vulnerability of adult neurons to hypoxic injury. Furthermore, we describe for the first time that treatment with the D-JNKI1, a JNK-inhibiting peptide, rescues adult hypoxic neurons from death and contributes to Hif-1α upregulation, probably via a direct interaction with the Hif-1α protein.
1H NMR-Based Metabolic Profiling Reveals the Effects of Fluoxetine on Lipid and Amino Acid Metabolism in Astrocytes

Fluoxetine, a selective serotonin reuptake inhibitor (SSRI), is a prescribed and effective antidepressant and generally used for the treatment of depression. Previous studies have revealed that the antidepressant mechanism of fluoxetine was related to astrocytes. However, the therapeutic mechanism underlying its mode of action in astrocytes remains largely unclear. In this study, primary astrocytes were exposed to 10 µM fluoxetine; 24 h post-treatment, a high-resolution proton nuclear magnetic resonance (1H NMR)-based metabolomic approach coupled with multivariate statistical analysis was used to characterize the metabolic variations of intracellular metabolites. The orthogonal partial least-squares discriminant analysis (OPLS-DA) score plots of the spectra demonstrated that the fluoxetine-treated astrocytes were significantly distinguished from the untreated controls. In total, 17 differential metabolites were identified to discriminate the two groups. These key metabolites were mainly involved in lipids, lipid metabolism-related molecules and amino acids. This is the first study to indicate that fluoxetine may exert antidepressant action by regulating the astrocyte’s lipid and amino acid metabolism. These findings should aid our understanding of the biological mechanisms underlying fluoxetine therapy.
Continued warming, salinification and oxygenation of the Greenland Sea gyre

Abstract The Greenland Sea gyre is one of the few areas where the water column is ventilated through open ocean convection. This process brings both anthropogenic carbon and oxygen from the atmosphere and surface ocean into the deep ocean, and also makes the Greenland Sea gyre interesting in a global perspective. In this study, a combination of ship- and float-based observations during the period 1986–2016 are analysed. Previous studies have shown warming and salinification of the upper 2000 m until 2011. The extended data record used here shows that this is continuing until 2016. In addition, oxygen concentrations are increasing over the entire period. The changes in temperature, salinity, and especially oxygen have been more pronounced since the turn of the century. This period has also been characterised by deeper wintertime mixed-layer depths, linking the warming, salinification and oxygenation to strengthened ventilation in the Greenland Sea gyre after 2000. The results also demonstrate that the strengthened ventilation can be tied to advection of warmer and more saline surface water from the North Atlantic through the Faroe-Shetland Channel. This advection has led to more saline surface waters in the Greenland Sea gyre, which is contributing to the deeper wintertime mixed layers.
The Xanthine Derivative KMUP-1 Inhibits Hypoxia-Induced TRPC1 Expression and Store-Operated Ca 2+ Entry in Pulmonary Arterial Smooth Muscle Cells

: Exposure to hypoxia results in the development of pulmonary arterial hypertension (PAH). An increase in the intracellular Ca 2+ concentration ([Ca 2+ ] i ) in pulmonary artery smooth muscle cells (PASMCs) is a major trigger for pulmonary vasoconstriction and proliferation. This study investigated the mechanism by which KMUP-1, a xanthine derivative with phosphodiesterase inhibitory activity, inhibits hypoxia-induced canonical transient receptor potential channel 1 (TRPC1) protein overexpression and regulates [Ca 2+ ] i through store-operated calcium channels (SOCs). Ex vivo PASMCs were cultured from Sprague-Dawley rats in a modular incubator chamber under 1% O 2 /5% CO 2 for 24 h to elucidate TRPC1 overexpression and observe the Ca 2+ release and entry. KMUP-1 (1 µ M) inhibited hypoxia-induced TRPC family protein encoded for SOC overexpression, particularly TRPC1. KMUP-1 inhibition of TRPC1 protein was restored by the protein kinase G (PKG) inhibitor KT5823 (1 µ M) and the protein kinase A (PKA) inhibitor KT5720 (1 µ M). KMUP-1 attenuated protein kinase C (PKC) activator phorbol 12-myristate 13-acetate (PMA, 1 µ M)-upregulated TRPC1. We suggest that the effects of KMUP-1 on TRPC1 might involve activating the cyclic guanosine monophosphate (cGMP)/PKG and cyclic adenosine monophosphate (cAMP)/PKA pathways and inhibiting the PKC pathway. We also used Fura 2-acetoxymethyl ester (Fura 2-AM, 5 µ M) to measure the stored calcium release from the sarcoplasmic reticulum (SR) and calcium entry through SOCs in hypoxic PASMCs under treatment with thapsigargin (1 µ M) and nifedipine (5 µ M). In hypoxic conditions, store-operated calcium entry (SOCE) activity was enhanced in PASMCs, and KMUP-1 diminished this activity. In conclusion, KMUP-1 inhibited the expression of TRPC1 protein and the activity of SOC-mediated Ca 2+ entry upon SR Ca 2+ depletion in hypoxic PASMCs.
Optimization modeling of speech timing

We present a novel paradigm for the computational modeling of speech timing. Our approach is based on two core assumptions: (1) the organization of speech is governed by the resolution of trade-offs between production and perception demands, and (2) isochrony at the syllable and stress group level, while not measurable in absolute terms in the speech signal, is present in a language-specific manner as an underlying tendency. These assumptions are implemented as an optimization procedure, minimizing a composite cost function whose components relate to durations of various prosodic constituents. The theoretical idea that much of the variation in speech can be explained as emerging from trade-offs between minimizing effort and maximizing perceptual clarity has been advocated most prominently by [2]. A recent computational implementation of this idea shows that various temporal coordination phenomena at the level of articulatory gestures can be accounted for on these grounds [3].
Racial differences in syndromal and subsyndromal depression in an older urban population.

OBJECTIVE The authors explored racial differences in the prevalence of depression and its associated factors among older persons. METHODS Using 1990 census data for Brooklyn, New York, the authors attempted to interview all cognitively intact persons age 55 years and older in randomly selected block groups. The sample was weighted by ethnicity and gender. The authors adapted George's Social Antecedent Model of Depression to allow examination of 20 independent variables and the nominal dependent variable consisting of three levels of depression. The data were analyzed with SUDAAN. RESULTS Syndromal depression was found among 8 percent of blacks and 10 percent of whites. Subsyndromal depression was found among 13 percent of blacks and 28 percent of whites. No racial differences were found in rates of syndromal depression, but significant racial differences were found in rates of subsyndromal depression and of any type of depression. Nonlinear effects on both types of depression were found, and higher levels of stress had a greater impact on whites than on blacks. The racial difference in subsyndromal depression was explained by its lower prevalence among French-speaking African Caribbeans. Many racial differences were found in the variables associated with syndromal and subsyndromal depression. CONCLUSIONS Race had an independent effect on the rate of subsyndromal depression and an interactive effect with stress on the rate of both syndromal and subsyndromal depression. For each racial group, different elements may play a role in the etiology, maintenance, and relief of depression. The findings underscore the importance of recognizing within-group and between-group racial differences in depression.
Parallel Gr ¨obner Basis Rewriting and Memory Optimization for Efﬁcient Multiplier Veriﬁcation

—Formal veriﬁcation of integer multipliers is a signiﬁ-cant but time-consuming problem. This paper introduces a novel approach that emphasizes the acceleration of symbolic computer algebra (SCA)-based veriﬁcation systems from the perspective of efﬁcient implementation instead of traditional algorithm enhancement. Our ﬁrst strategy involves leveraging parallel computing to accelerate the rewriting process of the Gr¨obner basis. Confronting the issue of frequent memory operations during the Gr¨obner basis reduction phase, we propose a double buffering scheme coupled with an operator scheduler to minimize memory allocation and deallocation. These unique contributions are integrated into a state-of-the-art veriﬁcation tool and result in substantial improvements in veriﬁcation speed, demonstrating more than 15 × speedup for a 1024 × 1024 multiplier.
Genetic Diversity of 41 Countries Phaseolus vulgaris L. Accessions, by ISSR Technique

The genetic diversity of 60 Phaseolus genotypes was investigated, which represented 41 countries around the world. Phaseolus vulgaris L. is the world’s second most important bean after soybeans; used for human food and animal feed. ISSR effectiveness in achievement of the genetic diversity among 60 common bean accessions. Into 2 major groups the studied Phaseolus vulgaris accessions were divided. Accessions of Asia and Europe seem to be more genetically similar (99%) to each other as they clustered in the same sub-group. The American and African varieties showed similarities as well and clustered in the same sub-tree group. In contrast, Asian and American accessions No. 22 and 23 showed high level of genetic similarities, although these were isolated from different regions. The phylogenetic tree showed that all the Asian accessions (along with Australian No. 59 and 60) were similar except Indian and Yemen accessions No. 9 and 20. Only Netherlands accession No. 3 was different from the rest of European accessions. Morocco accession No. 52 was genetically different from the rest of the African accessions. Canadian accession No. 44 seems to be different from the other North American accessions including Guatemala, Mexico and USA.
Impact of Protein Kinase PKR in Cell Biology: from Antiviral to Antiproliferative Action

SUMMARY The double-stranded RNA-dependent protein kinase PKR is a critical mediator of the antiproliferative and antiviral effects exerted by interferons. Not only is PKR an effector molecule on the cellular response to double-stranded RNA, but it also integrates signals in response to Toll-like receptor activation, growth factors, and diverse cellular stresses. In this review, we provide a detailed picture on how signaling downstream of PKR unfolds and what are the ultimate consequences for the cell fate. PKR activation affects both transcription and translation. PKR phosphorylation of the alpha subunit of eukaryotic initiation factor 2 results in a blockade on translation initiation. However, PKR cannot avoid the translation of some cellular and viral mRNAs bearing special features in their 5′ untranslated regions. In addition, PKR affects diverse transcriptional factors such as interferon regulatory factor 1, STATs, p53, activating transcription factor 3, and NF-κB. In particular, how PKR triggers a cascade of events involving IKK phosphorylation of IκB and NF-κB nuclear translocation has been intensively studied. At the cellular and organism levels PKR exerts antiproliferative effects, and it is a key antiviral agent. A point of convergence in both effects is that PKR activation results in apoptosis induction. The extent and strength of the antiviral action of PKR are clearly understood by the findings that unrelated viral proteins of animal viruses have evolved to inhibit PKR action by using diverse strategies. The case for the pathological consequences of the antiproliferative action of PKR is less understood, but therapeutic strategies aimed at targeting PKR are beginning to offer promising results.
Traumatic brain injury and alcohol/substance abuse: A Bayesian meta-analysis comparing the outcomes of people with and without a history of abuse

ABSTRACT Alcohol and substance (drugs and/or alcohol) abuse are major risk factors for traumatic brain injury (TBI); however, it remains unclear whether outcomes differ for those with and without a history of preinjury abuse. A meta-analysis was performed to examine this issue. The PubMed, Embase, and PsycINFO databases were searched for research that compared the neuroradiological, cognitive, or psychological outcomes of adults with and without a documented history of alcohol and/or substance abuse who sustained nonpenetrating TBIs. Data from 22 studies were analyzed using a random-effects model: Hedges’s g effect sizes measured the mean difference in outcomes of individuals with/without a history of preinjury abuse, and Bayes factors assessed the probability that the outcomes differed. Patients with a history of alcohol and/or substance abuse had poorer neuroradiological outcomes, including reduced hippocampal (g = −0.82) and gray matter volumes (g = −0.46 to −0.82), and enlarged cerebral ventricles (g = −0.73 to −0.80). There were limited differences in cognitive outcomes: Executive functioning (g = −0.51) and memory (g = −0.39 to −0.43) were moderately affected, but attention and reasoning were not. The findings for fine motor ability, construction, perception, general cognition, and language were inconclusive. Postinjury substance and alcohol use (g = −0.97 to −1.07) and emotional functioning (g = −0.29 to −0.44) were worse in those with a history of alcohol and/or substance abuse (psychological outcomes). This study highlighted the type and extent of post-TBI differences between persons with and without a history of alcohol or substance abuse, many of which may hamper recovery. However, variation in the criteria for premorbid abuse, limited information regarding the history of abuse, and an absence of preinjury baseline data prevented an assessment of whether the differences predated the TBI, occurred as a result of ongoing alcohol/substance abuse, or reflected the cumulative impact of alcohol/substance abuse and TBI.