Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Connectivity in Islets of Langerhans from Mouse Pancreas Tissue Slices

We propose a network representation of electrically coupled beta cells in islets of Langerhans. Beta cells are functionally connected on the basis of correlations between calcium dynamics of individual cells, obtained by means of confocal laser-scanning calcium imaging in islets from acute mouse pancreas tissue slices. Obtained functional networks are analyzed in the light of known structural and physiological properties of islets. Focusing on the temporal evolution of the network under stimulation with glucose, we show that the dynamics are more correlated under stimulation than under non-stimulated conditions and that the highest overall correlation, largely independent of Euclidean distances between cells, is observed in the activation and deactivation phases when cells are driven by the external stimulus. Moreover, we find that the range of interactions in networks during activity shows a clear dependence on the Euclidean distance, lending support to previous observations that beta cells are synchronized via calcium waves spreading throughout islets. Most interestingly, the functional connectivity patterns between beta cells exhibit small-world properties, suggesting that beta cells do not form a homogeneous geometric network but are connected in a functionally more efficient way. Presented results provide support for the existing knowledge of beta cell physiology from a network perspective and shed important new light on the functional organization of beta cell syncitia whose structural topology is probably not as trivial as believed so far.
Structural and Mechanical Features of Rapidly Solidified Al-2Fe-2Ni-5Mg Alloy

Rapid solidification (RS) of Al-2Fe-2Ni-5Mg alloy and following mechanical consolidation of powders by means of powder metallurgy (PM) methods was used with success to produce a bulk RS-material. RS powders were manufactured using an inert gas atomizing of the molten alloy and the spray deposition on the rotating water-cooled copper roll. Rods of 7 mm in diameter were received by means of the cold pressing of the flakes, vacuum degassing and hot extrusion method. For comparison purposes, the conventionally casted and hot extruded Al-2Fe-2Ni-5Mg alloy was tested as well. Mechanical properties of as-extruded materials were examined at 293 K – 873 K by compression tests performed at constant true strain rate of 5·10-3[s-1]. It was found that relatively high strength of as-extruded RS/PM material was accompanied by the high ductility of the samples deformed by hot compression tests. It was noticed that the most effective solution strengthening due to particles refining was observed at low deformation temperatures. Rising the test temperatures above ~ 420 K, was found to result in reduction of the flow stress to the values received for the industrial material (IM). The formation of coarse primary intermetallic compounds, which is typical for IM material, was effectively reduced for RS material. However some inhomogeneity of fine precipitates distribution in RS/PM material was observed. Nevertheless, it was considered that both solid solution hardening due to Mg addition and the dispersion strengthening due to refining of intermetallic compounds substantially increase the mechanical properties of the RS/PM material.
Phosphoinositide signaling plays a key role in cytokinesis

To perform the vital functions of motility and division, cells must undergo dramatic shifts in cell polarity. Recent evidence suggests that polarized distributions of phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate, which are clearly important for regulating cell morphology during migration, also play an important role during the final event in cell division, which is cytokinesis. Thus, there is a critical interplay between the membrane phosphoinositides and the cytoskeletal cortex that regulates the complex series of cell shape changes that accompany these two processes.
Induction of classical transplantation tolerance in the adult

Transplantation tolerance across histoincompatibilities in multiple non- H-2 minors (B10.BR into CBA/Ca) and "minor" plus H-2D (B10.A into CBA/Ca) antigens has been achieved successfully by combined adult bone marrow transplantation and treatment with CD4 and CD8 mAbs. The tolerant state was confirmed by permanent acceptance of donor strain skin grafts, and in vitro unresponsiveness to donor cells. Tolerance was associated with partial donor chimerism to various degrees. Tolerance to minor transplantation antigens induced in this manner was restricted to recipient-type MHC. The possibility was raised that tolerance resulted, at least in part, from clonal anergy rather than deletion.
Global synchronisation in translation invariant coupled map lattices

A suﬃcient condition for global synchronisation in coupled map lattices (CML) with translation invariant coupling and arbitrary individual map is proved. As in [Jost & Joy, 2001] where CML with reﬂection invariant couplings are considered, the condition only involves the linearised dynamics in the diagonal, namely for all points in the diagonal, the derivative must be contractive in all transverse directions. In addition to this result, a (weaker) condition that ensures the CML attractor to be composed of either 2-periodic or constant conﬁgurations, is also obtained.
Tagging accurately - Don’t guess if you know

We discuss combining knowledge-based (or rule-based) and statistical part-of-speech taggers. We use two mature taggers, ENGCG and Xerox Tagger, to independently tag the same text and combine the results to produce a fully disambiguated text. In a 27000 word test sample taken from a previously unseen corpus we achieve 98.5% accuracy. This paper presents the data in detail. We describe the problems we encountered in the course of combining the two taggers and discuss the problem of evaluating taggers.
MPD-RC 101 prospective study of reduced-intensity allogeneic hematopoietic stem cell transplantation in patients with myelofibrosis.

From 2007 to 2011, 66 patients with primary myelofibrosis or myelofibrosis (MF) preceded by essential thrombocythemia or polycythemia vera were enrolled into a prospective phase 2 clinical trial of reduced-intensity allogeneic hematopoietic stem cell transplantation (AHSCT), Myeloproliferative Disorder Research Consortium 101 trial. The study included patients with sibling donors (n = 32) receiving fludarabine/melphalan (FluMel) as a preparative regimen and patients with unrelated donors (n = 34) receiving conditioning with FluMel plus anti-thymocyte globulin (ATG). Patient characteristics in the 2 cohorts were similar. Engraftment occurred in 97% of siblings and 76% of unrelated transplants, whereas secondary graft failure occurred in 3% and 12%, respectively. With a median follow-up of 25 months for patients alive, the overall survival (OS) was 75% in the sibling group (median not reached) and 32% in the unrelated group (median OS: 6 months, 95% confidence interval [CI]: 3, 25) (hazard ratio 3.9, 95% CI: 1.8,8.9) (P < .001). Nonrelapse mortality was 22% in sibling and 59% in unrelated AHSCT. Survival correlated with type of donor, but not with the degree of histocompatibility match, age, or JAK2(V617F) status. In patients with MF with sibling donors, AHSCT is an effective therapy, whereas AHSCT from unrelated donors with FluMel/ATG conditioning led to a high rate of graft failure and limited survival. This trial was registered at www.clinicaltrials. gov as #NCT00572897.
DYNAMIC BITS AND PIECES

This report is the first of a planned sequence of annual updates of the book "Exploring Logical Dynamics", CSLI Publications, Stanford, summer 1996. It contains a number of further results obtained since its first publication. Sections 1, 2, 3 concern various issues in modal logic, 4, 5, 6 dynamic logic, and 7 temporal logic, while Sections 8, 9 digress into infinitary logic. Some corrigenda, and related results by others, have been included as well.
Homologous involvement of striatum and prefrontal cortex in rodent and human water maze learning

The multiple memory systems hypothesis posits that dorsal striatum and hippocampus are central nodes in independent memory systems, supporting response-based and place-based learning, respectively. Although our understanding of the function of hippocampus within this framework is relatively well established, the contribution of dorsal striatum is less clear. This in part seems to be due to the heterogeneous nature of dorsal striatum, which receives extensive topographically organized projections from higher cortical areas. Here we quantified neural activity in the intact brain while mice and humans acquired analogous versions of the Morris water maze. We found that dorsomedial striatum and medial prefrontal cortex support the initial acquisition of what is typically considered a hippocampus-dependent spatial learning task. We suggest that the circuit involving dorsomedial striatum and medial prefrontal cortex identified here plays a more task-independent role in early learning than currently thought. Furthermore, our results demonstrate that dorsomedial and dorsolateral striatum serve fundamentally different roles during place learning. The remarkably high degree of anatomical overlap in brain function between mouse and human observed in our study emphasizes the extent of convergence achievable with a well-matched multilevel approach.
Evidence for effective interventions to reduce mental health-related stigma and discrimination in the medium and long term: systematic review

Background Most research on interventions to counter stigma and discrimination has focused on short-term outcomes and has been conducted in high-income settings. Aims To synthesise what is known globally about effective interventions to reduce mental illness-based stigma and discrimination, in relation first to effectiveness in the medium and long term (minimum 4 weeks), and second to interventions in low- and middle-income countries (LMICs). Method We searched six databases from 1980 to 2013 and conducted a multi-language Google search for quantitative studies addressing the research questions. Effect sizes were calculated from eligible studies where possible, and narrative syntheses conducted. Subgroup analysis compared interventions with and without social contact. Results Eighty studies (n = 422 653) were included in the review. For studies with medium or long-term follow-up (72, of which 21 had calculable effect sizes) median standardised mean differences were 0.54 for knowledge and −0.26 for stigmatising attitudes. Those containing social contact (direct or indirect) were not more effective than those without. The 11 LMIC studies were all from middle-income countries. Effect sizes were rarely calculable for behavioural outcomes or in LMIC studies. Conclusions There is modest evidence for the effectiveness of anti-stigma interventions beyond 4 weeks follow-up in terms of increasing knowledge and reducing stigmatising attitudes. Evidence does not support the view that social contact is the more effective type of intervention for improving attitudes in the medium to long term. Methodologically strong research is needed on which to base decisions on investment in stigma-reducing interventions.
Structural Biology and Crystallization Communications the Structure of Haemophilus Influenzae Prephenate Dehydrogenase Suggests Unique Features of Bifunctional Tyra Enzymes

PDB Reference: chorismate mutase/prephenate dehydrogenase, 2pv7. Chorismate mutase/prephenate dehydrogenase from Haemophilus influenzae Rd KW20 is a bifunctional enzyme that catalyzes the rearrangement of chorismate to prephenate and the NAD(P) +-dependent oxidative decarboxyl-ation of prephenate to 4-hydroxyphenylpyruvate in tyrosine biosynthesis. The crystal structure of the prephenate dehydrogenase component (Hinf PDH) of the TyrA protein from H. influenzae Rd KW20 in complex with the inhibitor tyrosine and cofactor NAD + has been determined to 2.0 A ˚ resolution. Hinf PDH is a dimeric enzyme, with each monomer consisting of an N-terminal / dinucleotide-binding domain and a C-terminal-helical dimerization domain. The structure reveals key active-site residues at the domain interface, including His200, Arg297 and Ser179 that are involved in catalysis and/or ligand binding and are highly conserved in TyrA proteins from all three kingdoms of life. Tyrosine is bound directly at the catalytic site, suggesting that it is a competitive inhibitor of Hinf PDH. Comparisons with its structural homologues reveal important differences around the active site, including the absence of an – motif in Hinf PDH that is present in other TyrA proteins, such as Synechocystis sp. arogenate dehydrogenase. Residues from this motif are involved in discrimination between NADP + and NAD +. The loop between 5 and 6 in the N-terminal domain is much shorter in Hinf PDH and an extra helix is present at the C-terminus. Furthermore, HinfPDH adopts a more closed conformation compared with TyrA proteins that do not have tyrosine bound. This conformational change brings the substrate, cofactor and active-site residues into close proximity for catalysis. An ionic network consisting of Arg297 (a key residue for tyrosine binding), a water molecule, Asp206 (from the loop between 5 and 6) and Arg365 0 (from the additional C-terminal helix of the adjacent monomer) is observed that might be involved in gating the active site.
A replication study of a GWAS finding in migraine does not identify association in a Spanish case-control sample

Background: Migraine is a prevalent neurological disorder with a complex genetic background characterized by recurrent episodes of headache. The disease is subclassified into migraine with aura (MA) and migraine without aura (MO). Many association studies have been performed to date to identify genetic risk variants for common migraine, most of them focusing on selected candidate genes, with variable and often inconsistent results. Recently, a clinic-based genome-wide association study for migraine reported a functionally relevant risk variant (SNP rs1835740), involved in glutamate homeostasis, which showed a significant association with MA. We aimed to replicate this finding in a clinic-based study of a Spanish cohort with MA and MO patients. Methods: We genotyped SNP rs1835740 in a Spanish sample of 1521 patients and 1379 screened controls and performed a case-control association study. Conclusion: No association was found between the assayed SNP and any of the clinical groups considered.
Specificity of Tissue Transglutaminase Explains Cereal Toxicity in Celiac Disease

Celiac disease is caused by a selective lack of T cell tolerance for gluten. It is known that the enzyme tissue transglutaminase (tTG) is involved in the generation of T cell stimulatory gluten peptides through deamidation of glutamine, the most abundant amino acid in gluten. Only particular glutamine residues, however, are modified by tTG. Here we provide evidence that the spacing between glutamine and proline, the second most abundant amino acid in gluten, plays an essential role in the specificity of deamidation. On the basis of this, algorithms were designed and used to successfully predict novel T cell stimulatory peptides in gluten. Strikingly, these algorithms identified many similar peptides in the gluten-like hordeins from barley and secalins from rye but not in the avenins from oats. The avenins contain significantly lower percentages of proline residues, which offers a likely explanation for the lack of toxicity of oats. Thus, the unique amino acid composition of gluten and related proteins in barley and rye favors the generation of toxic T cell stimulatory gluten peptides by tTG. This provides a rationale for the observation that celiac disease patients are intolerant to these cereal proteins but not to other common food proteins.
The NUMAchine multiprocessor

Small-scale multiprocessors are becoming increasingly economical and common, whereas larger multiprocessors continue to have higher per-node costs. The NUMAchine multiprocessor project seeks to make large-scale multiprocessors more economical while maintaining high performance by exploring architectural and hardware features for low-cost, modular multiprocessors. To demonstrate our approach, we have implemented a prototype system that is scalable to 128 processors. An efficient directory-based cache coherence protocol exploits our hierarchical ring-based interconnect and supports sequential consistency. This paper documents the design choices and the resulting performance of the system using both simulation results and measurements on the prototype hardware.
Respiratory muscle stretch gymnastics in patients with post coronary artery bypass grafting pain: impact on respiratory muscle function, activity, mood and exercise capacity.

A new rehabilitation (New-RH) program including respiratory muscle stretch gymnastics (RMSG) was developed to alleviate post-coronary artery bypass grafting pain (PCP). Effects on respiratory muscle function, pain, activities of daily living (ADL), mood and exercise capacity were investigated. Subjects were 16 consecutive patients undergoing median full sternotomy coronary artery bypass grafting (CABG), and were randomly divided into equal New-RH (S-group) and conventional therapy (C-group) groups. Rib cage dominant breathing was observed postoperatively in both groups. With preoperative tan deltaVrc/deltaVab, increases at 1-week postoperatively and decreases at discharge for S-group tended to exceed those of C-group (p > .05). Decreased maximum inspiratory and expiratory pressure status for functional residual capacity and percent forced expiratory volume in one second at discharge again only tended to be smaller for S-group (p > .05). S-group displayed significantly reduced pain around both scapulas at discharge (p = .049), and increased mean overall ADL and profile of mood states (POMS)/Vigor scores (p = .031 and p = .018, respectively). POMS/Tension-Anxiety scores at discharge for S-group were significantly smaller than those preoperatively (p = .025), and S-group displayed significantly increased distance walked over 6-minutes at discharge than C-group (p = .029). New-RH improves patient participation in exercise therapy and increases exercise capacity by reducing PCP, relieving anxiety and tension, and improving ADL.
The genetics and pathology of mitochondrial disease

Mitochondria are double‐membrane‐bound organelles that are present in all nucleated eukaryotic cells and are responsible for the production of cellular energy in the form of ATP. Mitochondrial function is under dual genetic control – the 16.6‐kb mitochondrial genome, with only 37 genes, and the nuclear genome, which encodes the remaining ∼1300 proteins of the mitoproteome. Mitochondrial dysfunction can arise because of defects in either mitochondrial DNA or nuclear mitochondrial genes, and can present in childhood or adulthood in association with vast clinical heterogeneity, with symptoms affecting a single organ or tissue, or multisystem involvement. There is no cure for mitochondrial disease for the vast majority of mitochondrial disease patients, and a genetic diagnosis is therefore crucial for genetic counselling and recurrence risk calculation, and can impact on the clinical management of affected patients. Next‐generation sequencing strategies are proving pivotal in the discovery of new disease genes and the diagnosis of clinically affected patients; mutations in >250 genes have now been shown to cause mitochondrial disease, and the biochemical, histochemical, immunocytochemical and neuropathological characterization of these patients has led to improved diagnostic testing strategies and novel diagnostic techniques. This review focuses on the current genetic landscape associated with mitochondrial disease, before focusing on advances in studying associated mitochondrial pathology in two, clinically relevant organs – skeletal muscle and brain. © 2016 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
3 D INDUSTRIAL RECONSTRUCTION BY FITTING CSG MODELS TO A COMBINATION OF IMAGES AND POINT CLOUDS

We present a method for 3D reconstruction of industrial sites using a combination of images and point clouds with a motivation of achieving higher levels of automation, precision, and reliability. Recent advances in 3D scanning technologies have made possible rapid and cost-effective acquisition of dense point clouds for 3D reconstruction. As the point clouds provide explicit 3D information, they have a much higher potential for the automation of reconstruction. However, due to the measurement principle employed by laser scanners and their limited point density, the information on sharp edges is not very reliable. It is precisely where images have superiority over point clouds. In addition images are required for visual interpretation, texture mapping, and modelling parts not visible in the point clouds. Moreover, image acquisition is more flexible, and the cost and time required for it is much lower than that of laser scanning, making their combined use essential for a cost-effective solution. These reasons led us to develop a modelling strategy that uses both images and point clouds in combination with a library of CAD primitives found in industrial scenarios represented as CSG (Constructive Solid Geometry) objects. The modelling pipeline in our algorithm starts from point clouds as the main data source for automation. First of all we segment the point cloud using surface smoothness and detect simple objects like planes and cylinders using Hough Transform. This is followed by fitting of CSG objects to a combination of segments. These fitted CAD models are used as registration targets for adding more scans to the project. Additionally, by fitting the projected edges to image gradients we register images to point clouds. Once we have a registered data set, manual measurements are added to images to model missing parts and to increase the reliability of modelling for portions where laser data is known to be noisy. The final phase is similar to bundle adjustment in traditional Photogrammetry as there we estimate pose and shape parameters of all CSG objects using all image measurements and points clouds simultaneously. We name this final phase Integrated Adjustment as it integrates all available information to determine the unknown parameters. The results of applying this method to data from an industrial site are presented showing the complementary nature of point cloud and image data. An analysis of improvement in quality of 3D reconstruction shows the benefits of the adopted approach. * Corresponding author.