Miracle-dz/UniFAR-FTUs huggingface dataset:
A Comprehensive Approach to Disentangle the Effect of Cerebellar Damage on Physical Disability in Multiple Sclerosis

Cerebellar damage occurs frequently in multiple sclerosis (MS) patients, with a wide exhibition of symptoms particularly as impairments of balance and gait. Recent studies implementing new postprocessing magnetic resonance imaging (MRI) techniques showed how cerebellar subregional atrophy provides an explanation of disability in MS. The aim of this work was to evaluate the relationship between quantitative measures of physical disability, cerebellar subregional atrophy, and cerebellar peduncle disruption. Forty-nine MS patients and 32 healthy subjects as controls (HS) underwent a 3-Tesla MRI including 3D T1-weighted and diffusion tensor imaging. Patients underwent static posturography to calculate the body's center of pressure (COP) displacement, Expanded Disability Status Scale (EDSS), and 25-ft walking test (25-FWT). Cerebellar lobular volumes were automatically calculated using the Spatially Unbiased Infratentorial Toolbox. Tract-based spatial statistics (TBSS) in FSL was used to process diffusion tensor imaging (DTI) Fit-generated fractional anisotropy (FA) maps to assess structural connectivity of cerebellar peduncles. Stepwise multivariate linear regression analyses were used to explore relationships between variables. Cerebellar volumes (anterior and posterior, as well as lobular volumes from I to X) were significantly lower in patients with MS than HS (p < 0.05). FA in all cerebellar peduncles was lower in MS patients than in HS (p < 0.05). EDSS and 25-FWT showed an association with atrophy of lobule VIIIb (β = −0.37, p < 0.01, and β = −0.45, p < 0.001, respectively) COP measures inversely correlated with volume of lobules I–IV (β = −0.37, p < 0.01, and β = −0.36, p < 0.01). Lower FA in the three cerebellar peduncles of MS patients positively correlated with cerebellar lobular volumes. Our findings show how sensorimotor cerebellum atrophy and disruption of both afferent and efferent cerebellar connections contribute to physical disability in MS patients.
The influence of worm age, duration of exposure and endpoint selection on bioassay sensitivity for Neanthes arenaceodentata (Annelida: Polychaeta)

The influence of worm age, duration of exposure, and endpoint selection on bioassay sensitivity were evaluated for Neanthes arenaceodentata. Worms were exposed to contaminated sediment collected from Black Rock Harbor (BRH) near Bridgeport, Connecticut, USA. This sediment was diluted with clean control sediment to result in five experimental treatments: 0, 25, 50, 75, and 100% BRH. Three exposure scenarios were employed: (1) a 4‐week exposure beginning with newly emerged juveniles (EJ–4w), (2) a 7‐week exposure beginning with newly emerged juveniles (EJ–7w), and (3) a 4‐week exposure beginning with 3‐week‐old juveniles (3WO–4w). Six measures of worm size were recorded at the conclusion of each exposure to evaluate differences among measurement endpoints. Survival was significantly reduced at the 25% BRH level for the EJ–7w scenario and at the 100% BRH level for the EJ–4w and 3WO–4w scenarios. Growth was significantly reduced at the 25% BRH level in each exposure scenario. Estimates based on the calculated minimum detectable difference indicated that considerably lower concentrations of BRH (6–10%) should be distinguishable by measuring effects on Neanthes growth. Worm size measured in terms of projected area, dry weight, and ash‐free dry weight provided the most sensitive measures of effects. Increasing the length of exposure from 4 to 7 weeks and initiating exposures with emergent juveniles rather than 3‐week‐old worms increased the sensitivity of the bioassay. The results of this study demonstrate that N. arenaceodentata is sensitive to the presence of sediment‐associated contaminants and that test animal age, duration of exposure, and choice of endpoint can have a large effect on the magnitude of the toxic response observed.
Hydrogen distributions in marine sediments

Hydrogen concentrations have been measured in sulfate-reducing sediments of a British Colum- bian fjord and in Skan Bay, Alaska, as well as in the hemipclagic sediments of the eastern north tropical Pacific off the Mexican coast. In the sediments of both the Mexican shelf and Canadian fjord, hydrogen levels were lowest near the surface, increased with depth and reached a maximum pore-water concentration of about 25-35 nM before sulfate was totally depleted. Deeper in the sediments, H, levels decreased again. In Skan Bay sediments, concentrations of pore-water hydrogen increased almost linearly with depth to a maximum level of 60 nM. Measured rates of hydrogen production in Skan Bay sediments varied little with depth (about 200 nM d-l), and in Skan Bay the hydrogen pool had a turnover time of, at most, several hours. Model-predicted net rates of hydrogen production in Skan Bay are not significantly different than zero. These results are con- sistent with the hypothesis of interspecies hydrogen transfer between hydrogen-producing and -consuming bacterial populations, which predicts low ambient hydrogen concentrations and tight coupling between production and consumption. Carbon remineralization in anoxic envi- ronments proceeds through a series of bac- terially catalyzed redox reactions using var- ious inorganic compounds as electron acceptors. In agreement with thermody- namic predictions, oxygen is largely deplet- ed before nitrate reduction begins. In turn, nitrate reduction is followed by manganese dioxide, iron oxide, and sulfate reduction, and finally by reduction of carbon dioxide to methane (Froelich et al. 1979; Klinkham- mer 1980; Wilson et al. 1985). The molec- ular pathways, reaction rates, and processes controlling organic carbon remineralization are the subject of much research (see Ree- burgh 1983). Our work has focused on the distribution and cycling of hydrogen in sedimentary an- oxic systems. Molecular hydrogen (HZ) is an important intermediate in anaerobic carbon degradation because it can serve both as an electron source (2H+ + H2 + 2e-) or sink (HZ + 2e- 4 2H-I) during bacterially cata- lyzed redox reactions (Thauer et al. 1977). Some fermentation reactions which degrade
An Empirically Derived Trimodal Parameterization of Underwater Light in Complex Coastal Waters – A Case Study in the North Sea

As an essential parameter for all kinds of aquatic life, light influences life cycles and the behavior of various marine organisms. However, its primary role is that of a driver for photosynthesis and thus primary production, forming the basis of the marine food web. As a simplification when dealing with light, a common measure (e.g., used in biogeochemical models) is the photosynthetically active radiation (PAR), which integrates the spectral distribution of photon flux between 400 and 700 nm into a single value. While passing through the water column, light is attenuated by the water itself and its optically active substances (OAS) [e.g., phytoplankton, chromophoric dissolved organic matter (CDOM), and non-algal particles], summarized in the diffuse attenuation coefficient of downwelling radiation (Kd). Existing parameterizations for light attenuation in models often consider only phytoplankton as parameter, which is not sufficient for coastal areas where the contributions of CDOM and suspended mineral particles can be substantial. Furthermore, they mostly ignore the spectral variability of Kd by attenuating PAR with only a single coefficient. For this reason, this study proposes a parameterization of Kd that involves all relevant OAS and that attenuates PAR in three bands (trimodal approach). For this, the hyperspectral underwater light field was examined on three expeditions in different areas of the North Sea and along the British and Irish coasts. The derived Kd spectra were stepwise decomposed in the contributions of the different OAS and used in combination with direct OAS measurements to derive substance specific attenuation coefficients for the three bands. For comparison, also a monomodal and a spectral parameterization were developed. Evaluation showed that the trimodal approach was almost as accurate as the full spectral approach, while requiring only marginally more computational performance as the classical monomodal approach. Being therefore an excellent compromise between these factors, it can act as a valuable, yet computational affordable addition to biogeochemical models in order to improve their performance in coastal waters.
The magnitude and origins of storage losses in Nigerian yams

Experiments on the storage behaviour of yams (Dioscorea spp.) in the Eastern Region of Nigeria have shown that very serious losses of weight occur during even a few months' storage under normal Nigerian conditions, and that these losses are greatly enhanced when rotting of the tubers occurs, although they are little affected by sprouting. Water loss arising from desiccation of the tubers only accounts for a portion of the total loss. A limited degree of success has been achieved in reducing storage losses by fungicidal treatments.
The participative turn in Museum: The online facet

This study aims to explore the participative turn in Museums on social media, by analyzing the different stimulus that museums with complex code of access use to ‘democratize’ themselves through a social media platform and how effective they are according to the online public response. Empirically, the analysis is carried out in nine Italian Archaeological State Museums, as exemplars of museums with complex code of access, analyzing the content of their posts and the interactions generated over one year. Seven, out of the nine museums evaluated showed a misalignment between the online efforts and the community engagement. Online users value more posts related to the permanent collection of the museums than gathering practical information to visit the institution.
A Stable Grasping Method for Robotic Manipulator Based on Visual Detection

This paper proposes a stable grasping method for robotic manipulator based on visual detection. In this method, in order to eliminate the noise and get the obvious boundary of the target, firstly the obtained image is preprocessed. Secondly, according to the self-made template library, the optimal grasping point in image is obtained by template matching. Then, the proposed robotic grasping control method is used to convert the calculated grasping point in image into the control value of the robot, so as to complete the effective robotic grasping. Finally, the proposed method has a single image detection time of 17.25ms and a grasping success rate of 96.0%.
Assessment of Pentachlorophenol (PCP) Degrading Bacterial strains Isolated from the Tannery Effluent Sludge of Jajmau (India)

Pentachlorophenol is a toxic compound mainly use as preservative in leather and wood industries and also as disinfectant in various sectors such as agriculture, food, wood, oil and paints industries. In present investigation fifteen bacterial strains were isolated from sediment core of tannery effluent sludge (Kanpur, U.P., India). Eight strains were screened on mineral salt agar medium, containing sodium pentachlorophenate (Na-PCP) as a sole source of carbon and energy and bromothymol blue (0.1%) as screening agent. The screened strains were collectively enriched in lab scale chemostat at different concentration of PCP for 30 days and then were characterized morphologically as well as biochemically. The strains showed similarities with Pseudomonas species, Flavobacterium species (three strains of each), Proteus species and Bacillus species (one strains of each). PCP degrading potential of each individual species was performed in lab scale bioreactor for 40 hrs. It was observed that Flavobacterium species has highest PCP degrading potential as it degraded 55% PCP within 42 hours followed by Pseudomonas species and Bacillus species (47% and 44% respectively). The Proteus species showed lowest degradation potential (38%) within the same time whereas in control reactor 20% reduction was observed. Further, combination of different strains were designed for the assessment of consortia based comparative degradation of PCP in which combination of Flavobacterium species with Pseudomonas species showed significant reduction of 73% in PCP
Anti-inflammatory Activity of Lefamulin in a Lipopolysaccharide-Induced Lung Neutrophilia Model

Lefamulin is a novel pleuromutilin antibiotic approved for the treatment of community-acquired bacterial pneumonia. This study demonstrated anti-inflammatory activity of lefamulin in a murine lipopolysaccharide-induced lung neutrophilia model. Pretreatment of mice at clinically relevant lefamulin subcutaneous doses (35, 70, 140 mg/kg [free base]) followed by intranasal lipopolysaccharide challenge (5 μg/50 μL/mouse) demonstrated significant, dose-dependent reductions in total and neutrophil cell counts in bronchoalveolar lavage fluid samples, with reductions comparable to oral dexamethasone (0.5 mg/kg) pretreatment.
Amplification, Cloning and In silico Prediction of Full Length Elicitin Gene from Phytophthora capsici, the Causal Agent of Foot Rot Disease of Black Pepper

Elicitins are a family of small proteins secreted by Phytophthora, which induce leaf necrosis in infected plants. Here, we report the cloning of Elicitin gene from P. capsici, an Oomycete plant pathogen which causes significant damage to a broad range of host plants. Elicitin sequence was amplified using primers designed from the known Elicitin genes of other Phytophthora organisms based on their conserved motifs. The PCR amplified product size of 256 bp length and the BLAST analysis of the sequenced product showed perfect match with alpha-elicitin sequences of P. capsici. Subsequently, attempt was made to characterize the complete gene of elicitin from genome sequence information of P. capsici, by querying the amplified product against the genome. Local BLAST search against full genome identified entire coding sequence. Further sequence analysis identified promoter sequence, transcription start site, a leader signal sequence and a core elicitin domain, with a conserved 6 Cysteine residues. In addition, the three dimensional structure of capsicein was modelled, and the binding affinity of sterol and capsicein was studied using molecular docking. The developed model predicted strong binding affinity for Tyr 47.
Visual mismatch responses index surprise signalling but not expectation suppression

The ability to distinguish between commonplace and unusual sensory events is critical for efficient learning and adaptive behaviour. This has been investigated using oddball designs in which sequences of often-appearing (i.e. expected) stimuli are interspersed with rare (i.e. surprising) deviants. Resulting differences in electrophysiological responses following surprising compared to expected stimuli are known as visual mismatch responses (VMRs). VMRs are thought to index co-occurring contributions of stimulus repetition effects, expectation suppression (that occurs when one’s expectations are fulfilled), and expectation violation (i.e. surprise) responses; however, these different effects have been conflated in existing oddball designs. To better isolate and quantify effects of expectation suppression and surprise, we adapted an oddball design based on Fast Periodic Visual Stimulation (FPVS) that controls for stimulus repetition effects. We recorded electroencephalography (EEG) while participants (N=48) viewed stimulation sequences in which a single face identity was periodically presented at 6 Hz. Critically, one of two different face identities (termed oddballs) appeared as every 7th image throughout the sequence. The presentation probabilities of each oddball image within a sequence varied between 10-90%, such that participants could form expectations about which oddball face identity was more likely to appear within each sequence. We also included ‘expectation neutral’ 50% probability sequences, whereby consistently biased expectations would not be formed for either oddball face identity. We found that VMRs indexed surprise responses, and effects of expectation suppression were absent. That is, ERPs were more negative-going at occipitoparietal electrodes for surprising compared to neutral oddballs, but did not differ between expected and neutral oddballs. Surprising oddball-evoked ERPs were also highly similar across the 10-40% appearance probability conditions. Our findings indicate that VMRs which are not accounted for by repetition effects are best described as an all-or-none surprise response, rather than a minimisation of prediction error responses associated with expectation suppression. Highlights - We used a recently-developed oddball design that controls for repetition effects - We found effects of surprise but not expectation suppression on ERPs - Surprise responses did not vary by stimulus appearance probability
Undetectable Free Aromatic Amino Acids in Nails of Breast Carcinoma: Biomarker Discovery by a Novel Metabolite Purification VTGE System

Background: Metabolic reprogramming in breast cancer is depicted as a crucial change in the tumor microenvironment. Besides the molecular understanding of metabolic heterogeneity, appreciable attention is drawn to characterizing metabolite profiles in tumor tissue and derived biological fluids and tissue materials. Several findings reported on the metabolic alterations of free aromatic amino acids (FAAAs) and other metabolites in biological fluids. Furthermore, there is a significant gap in the development of a suitable method for the purification and analysis of metabolite biomarkers in nails of cancer patients. Methods: To address the metabolite alterations, specifically FAAA levels in nails, fingernail clippings of breast cancer patients (N = 10) and healthy subjects (N-12) were used for extraction and purification of metabolites. Here, we reported a novel and specifically designed vertical tube gel electrophoresis (VTGE) system that helped in the purification of metabolites in the range of 100–1,000 Da from nail materials. Here, the VTGE system uses 15% polyacrylamide under non-denaturing and non-reducing conditions, which makes eluted metabolites directly compatible with LC-HRMS and other analytical techniques. Qualitative and quantitative determination of FAAAs in nail lysates was done in positive ESI mode of the Agilent LC-HRMS platform. Results: The analysis on collected data of nail metabolites clearly suggested that FAAAs including tryptophan, tyrosine, phenylalanine, and histidine were undetectable in nail lysates of breast cancer over healthy subjects. This is a first report that showed highly reduced levels of FAAAs in nails of breast cancer patients. Furthermore, the present observation is in consonance with previous findings that showed cancer cachexia and high amino acid catabolism in breast cancer patients that drive metabolite-led cancer growth and proliferation. Conclusion: This paper provides a proof of concept for a novel and specifically developed VTGE process that showed first evidence on the undetectable level of FAAAs in nails of breast cancer patients as metabolite biomarkers. Here, the authors propose the potential use of a VTGE-assisted process to achieve metabolomic discovery in nails of breast cancer and other tumor types.
Automatic decomposition of mixed integer programs for lagrangian relaxation using a multiobjective approach

This paper presents a new method to automatically decompose general Mixed Integer Programs (MIPs). To do so, we represent the constraint matrix for a general MIP problem as a hypergraph and relax constraints by removing hyperedges from the hypergraph. A Breadth First Search algorithm is used to identify the individual partitions that now exist and the resulting decomposed problem. We propose that good decompositions have both a small number of constraints relaxed and small subproblems in terms of the number of variables they contain. We use the multiobjective Nondominated Sorting Genetic Algorithm II (NSGA-II) to create decompositions which minimize both the size of the subproblems and the number of constraints relaxed. We show through our experiments the types of decompositions our approach generates and test empirically the effectiveness of these decompositions in producing bounds when used in a Lagrangian Relaxation framework. The results demonstrate that the bounds generated by our decompositions are significantly better than those attained by solving the Linear Programming relaxation, as well as the bounds found via random and greedy constraint relaxation and decomposition generation.
Ouroboros: virtualized queues for dynamic memory management on GPUs

Dynamic memory allocation on a single instruction, multiple threads architecture, like the Graphics Processing Unit (GPU), is challenging and implementation guidelines caution against it. Data structures must rise to the challenge of thousands of concurrently active threads trying to allocate memory. Efficient queueing structures have been used in the past to allow for simple allocation and reuse of memory directly on the GPU but do not scale well to different allocation sizes, as each requires its own queue. In this work, we propose Ouroboros, a virtualized queueing structure, managing dynamically allocatable data chunks, whilst being built on top of these same chunks. Data chunks are interpreted on-the-fly either as building blocks for the virtualized queues or as paged user data. Re-usable user memory is managed in one of two ways, either as individual pages or as chunks containing pages. The queueing structures grow and shrink dynamically, only currently needed queue chunks are held in memory and freed up queue chunks can be reused within the system. Thus, we retain the performance benefits of an efficient, static queue design while keeping the memory requirements low. Performance evaluation on an NVIDIA TITAN V with the native device memory allocator in CUDA 10.1 shows speed-ups between 11X and 412X, with an average of 118X. For real-world testing, we integrate our allocator into faimGraph, a dynamic graph framework with proprietary memory management. Throughout all memory-intensive operations, such as graph initialization and edge updates, our allocator shows similar to improved performance. Additionally, we show improved algorithmic performance on PageRank and Static Triangle Counting. Overall, our memory allocator can be efficiently initialized, allows for high-throughput allocation and offers, with its per-thread allocation model, a drop-in replacement for comparable dynamic memory allocators.
The NF-κB Signaling Pathway, the Microbiota, and Gastrointestinal Tumorigenesis: Recent Advances

Gastrointestinal (GI) cancers, especially gastric cancer and colorectal cancer (CRC), represent a major global health burden. A large population of microorganisms residing in the GI tract regulate physiological processes, such as the immune response, metabolic balance, and homeostasis. Accumulating evidence has revealed the alteration of microbial communities in GI tumorigenesis. Experimental studies in cell lines and animal models showed the functional roles and molecular mechanisms of several bacteria in GI cancers, including Helicobacter pylori in gastric cancer as well as Fusobacterium nucleatum, Escherichia coli, Peptostreptococcus anaerobius, and Bacteroides fragilis in CRC. The transcriptional factor NF-κB plays a crucial role in the host response to microbial infection through orchestrating innate and adaptive immune functions. Moreover, NF-κB activity is linked to GI cancer initiation and development through its induction of chronic inflammation, cellular transformation and proliferation. Here, we provide an overview and discussion of modulation of the NF-κB signaling pathway by microbiota, especially infectious bacteria, in GI tumorigenesis, with a major focus on gastric cancer and CRC.