Miracle-dz/UniFAR-FTUs huggingface dataset:
Depletion of the membrane-fusion regulator Munc18c attenuates caerulein hyperstimulation–induced pancreatitis

Epithelial pancreatic acinar cells perform crucial functions in food digestion, and acinar cell homeostasis required for secretion of digestive enzymes relies on SNARE-mediated exocytosis. The ubiquitously expressed Sec1/Munc18 protein mammalian uncoordinated-18c (Munc18c) regulates membrane fusion by activating syntaxin-4 (STX-4) to bind cognate SNARE proteins to form a SNARE complex that mediates exocytosis in many cell types. However, in the acinar cell, Munc18c's functions in exocytosis and homeostasis remain inconclusive. Here, we found that pancreatic acini from Munc18c-depleted mice (Munc18c+/−) and human pancreas (lenti-Munc18c-shRNA–treated) exhibit normal apical exocytosis of zymogen granules (ZGs) in response to physiologic stimulation with the intestinal hormone cholecystokinin (CCK-8). However, when stimulated with supraphysiologic CCK-8 levels to mimic pancreatitis, Munc18c-depleted (Munc18c+/−) mouse acini exhibited a reduction in pathological basolateral exocytosis of ZGs resulting from a decrease in fusogenic STX-4 SNARE complexes. This reduced basolateral exocytosis in part explained the less severe pancreatitis observed in Munc18c+/− mice after hyperstimulation with the CCK-8 analog caerulein. Likely as a result of this secretory blockade, Munc18c-depleted acini unexpectedly activated a component of the endoplasmic reticulum (ER) stress response that contributed to autophagy induction, resulting in downstream accumulation of autophagic vacuoles and autolysosomes. We conclude that Munc18c's role in mediating ectopic basolateral membrane fusion of ZGs contributes to the initiation of CCK-induced pancreatic injury, and that blockade of this secretory process could increase autophagy induction.
Logarithmic transformation of spectral-domain optical coherence tomography data in uveitis-associated macular edema.

PURPOSE To determine the utility of logarithmic transformation of spectral-domain optical coherence tomography (logSD-OCT) retinal thickness data for assessment of clinically meaningful changes in uveitis-associated macular edema. METHODS Patients with noninfectious uveitis-associated macular edema at our institution between August 2010 and March 2011 were identified. Only those with SD-OCT imaging were included. The clinical diagnoses, visual acuities, and central subfield thickness (CST) measurements were recorded. Logarithmic transformation of the retinal thickness was performed and frequency histograms plotted. A linear mixed-effects model of the logarithm minimum angle of resolution (logMAR) visual acuity on logSD-OCT was created to account for within-patient correlation among visits and between eyes. RESULTS A total of 98 SD-OCT images from 34 patients were analyzed. The mean age at examination was 40 years (range, 11-69 years). Anatomic diagnoses included anterior/intermediate uveitis (23%), intermediate uveitis (21%), posterior uveitis (12%), and panuveitis (44%). LogSD-OCT data provided a more normal distribution than standard CST. Skewness and kurtosis of CST data were 1.04 and 0.37, respectively, and skewness and kurtosis of logSD-OCT data were 0.40 and -0.48, respectively. There was a positive correlation between logSD-OCT and logMAR visual acuity. Specifically, for each 0.1-unit increase in logSD-OCT, the logMAR visual acuities increased (worsened) by 0.082 units (95% CI: 0.057-0.107, P < 0.001). CONCLUSIONS Logarithmic transformation of SD-OCT measurements provided a more normal distribution and positively correlated with logMAR visual acuity. This transformation of retinal thickness may be valuable for assessing clinically significant changes in SD-OCT measurements in future uveitis studies.
Efficacy of D5F3 IHC for detecting ALK gene rearrangement in NSCLC patients: a systematic review and meta-analysis

We conducted a pooled analysis comparing the efficacy of an immunohistochemistry (IHC) assay using the D5F3 antibody with that of fluorescence in situ hybridization (FISH) for detecting ALK gene rearrangement in NSCLC patients. A total of 32 studies involving 5805 samples were included in this review. Pooled sensitivity for D5F3 IHC was 0.97 (95%CI: 0.93-0.98), specificity was 0.99 (95%CI: 0.98-1.00), PLR was 119.20 (95%CI: 57.79-245.89), NLR was 0.03 (95%CI: 0.02-0.07), DOR was 3526.66 (95%CI: 1344.71-9249.03), and AUROC was 1.00 (95%CI: 0.99-1.00). Meta-regression revealed that specimen type was a source of heterogeneity for specificity, and specimen type and FISH signal distance were sources of heterogeneity in the joint model. Subgroup analysis revealed that sensitivity and specificity were higher when the FISH signal distance standard was ≥ 2 than when it was ≥ 1. Sensitivity was higher for tumor specimens than for cell specimens; specificity was higher for cell specimens than for tumor specimens. In conclusion, the D5F3 IHC assay was nearly as effective as FISH for detection of ALK gene rearrangement in NSCLC patients.
Towards a Contingency Theory based Model of the Influence of Regulation on MIS

In modern societies and in particular since the financial crisis legal requirements and regulations get more and more attention. The massive amount of regulations also affects management information systems (MIS) with an impact on both, the system level as well as the organizational level. To consider all these regulations is a challenging task for organizations which handle regulative complexity in different ways. Until now, the influence of the degree of regulation on the organization of MIS received only little attention in IS research. This paper introduces a theoretical model and research design that enables investigating the influence of regulation on the organization and success of MIS. The presented model is based on the contingency theory.
Safe and Effective Sarcoma Therapy through Bispecific Targeting of EGFR and uPAR

Sarcomas differ from carcinomas in their mesenchymal origin. Therapeutic advancements have come slowly, so alternative drugs and models are urgently needed. These studies report a new drug for sarcomas that simultaneously targets both tumor and tumor neovasculature. eBAT is a bispecific angiotoxin consisting of truncated, deimmunized Pseudomonas exotoxin fused to EGF and the amino terminal fragment of urokinase. Here, we study the drug in an in vivo “ontarget” companion dog trial as eBAT effectively kills canine hemangiosarcoma and human sarcoma cells in vitro. We reasoned the model has value due to the common occurrence of spontaneous sarcomas in dogs and a limited lifespan allowing for rapid accrual and data collection. Splenectomized dogs with minimal residual disease were given one cycle of eBAT followed by adjuvant doxorubicin in an adaptive dose-finding, phase I–II study of 23 dogs with spontaneous, stage I–II, splenic hemangiosarcoma. eBAT improved 6-month survival from <40% in a comparison population to approximately 70% in dogs treated at a biologically active dose (50 μg/kg). Six dogs were long-term survivors, living >450 days. eBAT abated expected toxicity associated with EGFR targeting, a finding supported by mouse studies. Urokinase plasminogen activator receptor and EGFR are targets for human sarcomas, so thorough evaluation is crucial for validation of the dog model. Thus, we validated these markers for human sarcoma targeting in the study of 212 human and 97 canine sarcoma samples. Our results support further translation of eBAT for human patients with sarcomas and perhaps other EGFR-expressing malignancies. Mol Cancer Ther; 16(5); 956–65. ©2017 AACR.
Microsatellite markers reveal multiple origins for Italian weedy rice

Weedy rice (Oryza sativa L.) is one of the major issues of rice cultivation worldwide. In Italy, it infests about 70% of the total rice area. Different Weedy Rice populations can be distinguished based on variable morphological and physiological traits; however, little is known about genetic differentiation and origin of Italian weedy rice populations. The objective of this study was to genetically and morphologically characterize and compare different Italian weedy rice populations selected on the basis of different phenotypes. The main Italian rice territory was divided into 10 geographical areas in which 40 weedy rice populations were collected and grouped according to the awn traits. All the individuals of the populations were morphologically characterized according to plant and seed traits. Genetic characterization was performed using 19 SSR markers on all the collected accessions, and several rice cultivars, including some very old (late 19th century), nowadays are no longer cultivated. ANOVA showed that morphological plant and seed traits were significantly affected by the collection area and awnedness group. The importance of the awn morphology was also reflected in the Bayesian clustering where, despite a relatively low genetic diversity, the clusters displayed different awn types. An UPGMA dendrogram confirmed the clusters detected in STRUCTURE analysis and also revealed a grouping of certain old cultivars with the weedy rice, suggesting a common origin.
EVALUATION OF A ROTATING DISK APPARATUS: DRAG OF A DISK ROTATING IN A VISCOUS FLUID

Abstract : A rotating disk apparatus, designed to attain high shear stresses comparable to those about hulls of full-scale ships is evaluated. Shear stresses were not measured but were inferred from measurements of disk moments. Two disk surfaces were evaluated, hydraulically smooth and sandpaper rough. For the smooth and rough surface disks in air, the experimental moment coefficients were generally greater than the theoretical predictions. Only the smooth surface disk in water gave results lower than predictions.
What and where: a Bayesian inference theory of visual attention

In the theoretical framework described in this thesis, attention is part of the inference process that solves the visual recognition problem of what is where. The theory proposes a computational role for attention and leads to a model that predicts some of its main properties at the level of psychophysics and physiology. In our approach, the main goal of the visual system is to infer the identity and the position of objects in visual scenes: spatial attention emerges as a strategy to reduce the uncertainty in shape information while feature-based attention reduces the uncertainty in spatial information. Featural and spatial attention represent two distinct modes of a computational process solving the problem of recognizing and localizing objects, especially in difficult recognition tasks such as in cluttered natural scenes. We describe a specific computational model and relate it to the known functional anatomy of attention. We show that several well-known attentional phenomena—including bottom-up pop-out effects, multiplicative modulation of neuronal tuning curves and shift in contrast responses—emerge naturally as predictions of the model. We also show that the bayesian model predicts well human eye fixations (considered as a proxy for shifts of attention) in natural scenes. Finally, we demonstrate that the same model, used to modulate information in an existing feedforward model of the ventral stream, improves its object recognition performance in clutter. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
Simultaneous Hand–Eye, Tool–Flange, and Robot–Robot Calibration for Comanipulation by Solving the $\mathbf{AXB=YCZ}$ Problem

Multirobot comanipulation shows great potential in surpassing the limitations of single-robot manipulation in complicated tasks such as robotic surgeries. However, a dynamic multirobot setup in unstructured environments poses great uncertainties in robot configurations. Therefore, the coordination relationships between the end-effectors and other devices, such as cameras (hand-eye calibration) and tools (tool-flange calibration), as well as the relationships among the base frames (robot-robot calibration) have to be determined timely to enable accurate robotic cooperation for the constantly changing configuration of the systems. We formulated the problem of hand-eye, tool-flange, and robot-robot calibration to a matrix equation AXB=YCZ. A series of generic geometric properties and lemmas were presented, leading to the derivation of the final simultaneous algorithm. In addition to the accurate iterative solution, a closed-form solution was also introduced based on quaternions to give an initial value. To show the feasibility and superiority of the simultaneous method, two nonsimultaneous methods were compared through thorough simulations under various robot movements and noise levels. Comprehensive experiments on real robots were also performed to further validate the proposed methods. The comparison results from both simulations and experiments demonstrated the superior accuracy and efficiency of the proposed simultaneous calibration method.
A 125 kDa RNase E/G-like protein is present in plastids and is essential for chloroplast development and autotrophic growth in Arabidopsis

Endoribonuclease E (RNase E) is a regulator of global gene expression in Escherichia coli and is the best studied member of the RNase E/G ribonuclease family. Homologues are present in other bacteria but the roles of plant RNase E/G-like proteins are not known. Arabidopsis thaliana contains a single nuclear gene (At2g04270) encoding a product with the conserved catalytic domain of RNase E/G-like proteins. At2g04270 and the adjacent At2g04280 gene form converging transcription units with a ∼40 base overlap at their 3’ ends. Several translation products were predicted from the analyses of At2g04270 cDNAs. An antibody raised against a recombinant A. thaliana RNase E/G-like protein recognized a 125 kDa protein band in purified chloroplast preparations fractionated by SDS-PAGE. The 125 kDa RNase E/G-like protein was detected in cotyledons, rosette and cauline leaves. T-DNA insertions in exon 6 or intron 11 of At2g04270 result in loss of the 125 kDa band or truncation to a 110 kDa band. Loss of At2g04270 function resulted in the arrest of chloroplast development, loss of autotrophic growth, and reduced plastid ribosomal, psbA and rbcL RNA levels. Homozygous mutant plants were pale-green, contained smaller plastids with fewer thylakoids and shorter granal stacks than wild-type chloroplasts, and required sucrose at all growth stages following germination right up to flowering and setting seeds. Recombinant A. thaliana RNase E/G-like proteins rescued an E. coli RNase E mutant and cleaved an rbcL RNA substrate. Expression of At2g04270 was highly correlated with genes encoding plastid polyribonucleotide phosphorylase, S1 RNA-binding, and CRS1/YhbY domain proteins.
Opportunistic Routing in Intermittently Connected Mobile P2P Networks

Mobile P2P networking is an enabling technology for mobile devices to self-organize in an unstructured style and communicate in a peer-to-peer fashion. Due to user mobility and/or the unrestricted switching on/off of the mobile devices, links are intermittently connected and end-to-end paths may not exist, causing routing a very challenging problem. Moreover, the limited wireless spectrum and device resources together with the rapidly growing number of portable devices and amount of transmitted data make routing even harder. To tackle these challenges, the routing algorithms must be scalable, distributed, and light-weighted. Nevertheless, existing approaches usually cannot simultaneously satisfy all these three requirements. In this paper, we propose two opportunistic routing algorithms for intermittently connected mobile P2P networks, which exploit the spatial locality, spatial regularity, and activity heterogeneity of human mobility to select relays. The first algorithm employs a depth-search approach to diffuse the data towards the destination. The second one adopts a depth-width-search approach in a sense that it diffuses the data not only towards the destination but also to other directions determined by the actively moving nodes (activists) to find better relays. We perform both theoretical analysis as well as a comparison based simulation study. Our results obtained from both the synthetic data and the real world traces reveal that the proposed algorithms outperform the state-of-the-art in terms of delivery latency and delivery ratio.
The Benefit of Adjuvant Radiotherapy in High-grade Nonmetastatic Retroperitoneal Soft Tissue Sarcoma: A SEER Analysis

Objectives: Controversy persists on the use of adjuvant radiotherapy (RT) in patients with retroperitoneal sarcoma (RPS). High-grade disease is known to be associated with decreased local control and overall survival (OS). Because RT has proven beneficial for local control and OS in patients with high-grade extremity soft tissue sarcoma, we evaluated the efficacy of adjuvant RT in high-grade RPS. Methods: The Surveillance, Epidemiology, and End Results database was used to identify patients with pathology-confirmed RPS from 1973 to 2010. Clinical characteristics and outcomes were analyzed. Results: Of 480 total patients, 144 (30.0%) received postoperative radiation. Patients who received adjuvant RT had improved median OS (36 mo) compared with those who did not (27 mo, hazard ratio [HR]=0.79, P=0.023). On multivariate analysis the use of adjuvant RT (HR=0.80; 95% confidence interval [CI], 0.65-0.98; P=0.029), male sex (HR=1.32; 95% CI, 1.10-1.59; P=0.003), age above 65 years (HR=1.38; 95% CI, 1.15-1.67; P=0.001), and increasing the Surveillance, Epidemiology, and End Results historical stage (HR=1.46; 95% CI, 1.21-1.76; P<0.001) were all prognostic factors for OS. Conclusions: In a large retrospective analysis, postoperative RT improved OS in high-grade RPS patients. As such, adjuvant RT should be strongly considered in all patients with high-grade RPS. The optimal timing of RT relative to surgery requires further study.
Improvements of the Tensile Strength of Phenolic Resin Adhesive by Surface-Modified Nanocrystalline Cellulose

In this study, the tensile strength of phenolic resin adhesive was reinforced by the use of surface-modified nanocrystalline cellulose (NCC). The original NCC was modified by 3-methacryloxy-propyltrimethoxysilane (MPS) to improve the wetting property with the phenolic resin adhesive. The phenolic resin adhesive with surface-modified NCC was analyzed by Fourier transform infrared (FT-IR). Tensile strength of the modified phenolic resin adhesive was tested according to Chinese National Standard GB/T 2567-2008. The results showed that the wetting property between NCC modified by MPS and phenolic resin adhesive was increased by 21.7% and the tensile strength of phenolic resin adhesive with modified NCC was enhanced from 6.25 MPa to 15.97 MPa.
An Effective Occipitomental View Enhancement Based on Adaptive Morphological Texture Analysis

This paper aims to present an algorithm that specifically enhances maxillary sinuses using a novel contrast enhancement technique based on the adaptive morphological texture analysis for occipitomental view radiographs. First, the skull X-ray (SXR) is decomposed into rotational blocks (RBs). Second, each RB is rotated into various directions and processed using morphological kernels to obtain the dark and bright features. Third, a gradient-based block segmentation decomposes the interpolated feature maps into feature blocks (FBs). Finally, the histograms of FBs are equalized and overlaid locally to the input SXR. The performance of the proposed method was evaluated on an independent dataset, which comprises of 145 occipitomental view-based human SXR images. According to the experimental results, the proposed method is able to increase the diagnosis accuracy by 83.45% compared with the computed tomography modality as the gold standard.
Patient Preferences and Acceptability of Evidence-Based and Novel Treatments for Obsessive-Compulsive Disorder.

OBJECTIVE This study examined preferences for and acceptability of treatments for obsessive-compulsive disorder (OCD). METHODS Through an online survey, adults who self-reported OCD chose their preferred evidence-based treatments, rated acceptability of novel treatments, and answered open-ended questions about their preferences. Analyses examined associations between demographic, clinical, and treatment variables and first-line and augmentation treatment preferences. Latent class analysis (LCA) explored whether distinct profiles among participants predicted preferences. Data from open-ended questions were analyzed by using qualitative methods. RESULTS Among 216 adults with at least moderate OCD symptoms, first-line preferences for exposure and response prevention (EX/RP) and serotonin reuptake inhibitor (SRI) medications were similar (55% and 45%). However, EX/RP was significantly preferred over antipsychotic medication as an augmentation treatment for SRIs (68% and 31%; p<.001). Regarding first-line preferences, no factors were associated with EX/RP preference, but participants who preferred SRIs were currently receiving OCD treatment (p=.011) or taking SRIs (p<.001) and reported a positive treatment experience overall (p=.043) and with medications (p<.001). Participants who preferred EX/RP as augmentation treatment were younger (p<.001) and female (p=.021) and taking benzodiazepines (p=.050). LCA analyses generated two distinct profiles, one of which preferred SRIs: those with a history of OCD diagnosis and treatment, higher income, and private insurance (p=.001). For novel treatments, acceptance and commitment therapy was the most acceptable and deep brain stimulation the least. CONCLUSIONS Preferences for OCD treatments varied by individual characteristics. Future research should examine whether incorporating preferences into treatment planning has an impact on clinical care.
Modeling and Characterization of Recompressed Damaged Materials

Ductile metals subjected to shock loading can develop internal damage through nucleation growth and coalescence of voids. The extent of damage can range from a well-defined spall plane induced by light shocks to more widespread damage caused by strong shocks. Because damage materials are often part of a dynamic system, significant additional deformation can occur in extensively damaged materials. To represent material behavior in simulation codes for stockpile stewardship calculations, both the damage and the recompression processes must be modeled accurately. Currently, no experimentally based models of recompression behavior are available for use in numerical simulations. The goals of this project are to (1) perform recompression experiments on samples containing controlled and well-characterized damage, (2) develop a model capturing the recompression behavior and residual strength based on the experimental data and micro-mechanical models, and (3) implement the model in an Advanced Simulation and Computing (ASCI) code (ALE3D). The recompression model, together with failure models based on underlying physical mechanisms, will provide a more accurate representation of material behavior-information that is needed for simulations of explosively loaded materials such as those required by the Stockpile Stewardship Program.
Vocal tremor: where are we at?

Purpose of review Vocal tremor in movement disorders is often overlooked, although it has a significant impact on quality of life. Careful observation of tremor phenomenology allows for accurate diagnosis and tailored treatment. Recent findings The central pathways associated with various vocal tremor-associated diseases have been further elucidated. Summary Patients are likely to benefit from a combination of medical and interventional treatments delivered within a multidisciplinary setting