Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of assay epitope specificity in gastrinoma diagnosis.

The antral hormone gastrin regulates gastric acid secretion and growth of the gastric mucosa (1). As a result of the elaborate cellular maturation process of progastrin, the antral G cells release a mixture of different acid-stimulatory gastrins and other precursor fragments to the circulation (2). This mixture comprises gastrin-71, -52, -34, -17, -14, and -6, all of which are carboxyamidated and circulate in an O-sulfated and nonsulfated form. The dominant gastrin forms in serum from healthy humans are amidated gastrin-34 and -17 [for a review, see Ref. (3)]. In cases of increased gastrin synthesis, however, as seen in patients with hypo- and achlorhydric gastritis and gastrin-producing tumors, i.e., gastrinomas, the serum or plasma pattern molecular pattern changes to larger molecular forms and more incompletely processed precursors (4)(5)(6). Hence, only little gastrin-17 may be present in serum from hypergastrinemic patients, although gastrin-17 is the predominant tissue form in healthy antral mucosa. In clinical chemistry, the only well-indicated routine use of gastrin assays is in the diagnosis of gastrinomas, i.e., the Zollinger–Ellison syndrome (7)(8). Gastrin assays for diagnostic purposes (usually RIA or ELISA) should preferably measure all forms of gastrin. Although assays specific for only one molecular gastrin form may be of interest in biochemical research, such assays pose a significant diagnostic problem. In the following, …
Direction-of-arrival estimation under noisy condition using four-line omni-directional microphones mounted on a robot head

We propose a new direction-of-arrival (DOA) estimation method suitable for autonomous mobile robots. Autonomous mobile robots have to meet physical constraints of signal processing devices, such as a space-saving microphone arrangement and few computational resources. In addition, DOA estimation of the robots needs to be robust to noise around the robots. In order to cope with the physical constraints, we used four-line omni-directional micro mechanical systems (MEMS) microphones. DOA estimation was conducted using statistical pattern recognition in which normalized spectral amplitudes, which were free from sound sources, were used as DOA features. In the proposed method, strict head related transfer function estimation, which is not practically feasible, is not needed. In addition, unlike many conventional methods, phase information is not explicitly used because the phase information is unreliable in the situation that we deal with, i.e., situations in which the microphone spacings are small, or strong reflections and diffractions occur around the microphones. The feature vectors we used can cope with these problems. Effectiveness of the proposed method was experimentally investigated in recognition of 19 DOAs in the presence of diffuse noise: the proposed method achieved a DOA correct of approximately 99% at a SNR of 0 dB.
Real-time visualization of scalably large collections of heterogeneous objects

This paper presents results for real-time visualization of out-of-core collections of 3D objects. This is a significant extension of previous methods and shows the generality of hierarchical paging procedures applied both to global terrain and any objects that reside on it. Applied to buildings, the procedure shows the effectiveness of using a screen-based paging and display criterion within a hierarchical framework. The results demonstrate that the method is scalable since it is able to handle multiple collections of buildings (e.g., cities) placed around the earth with full interactivity and without extensive memory load. Further the method shows efficient handling of culling and is applicable to larger, extended collections of buildings. Finally, the method shows that levels of detail can be incorporated to provide improved detail management.
Use of the MGB Eclipse System and SmartCycler PCR for Differentiation of Mycobacterium chelonae and M. abscessus

ABSTRACT Although accurate in the identification of Mycobacterium species, partial 16S rRNA gene sequencing does not distinguish Mycobacterium chelonae from M. abscessus. Thus, we designed a SmartCycler PCR assay targeting the 16S-to-23S internal transcribed spacer (ITS) region with use of MGB Eclipse probes to distinguish each species. Comparison with PCR-restriction enzyme analysis of a 441-bp fragment of the hsp65 gene resulted in 100% correlation with 25 isolates of M. chelonae and 25 isolates of M. abscessus. ITS PCR performed on 90 consecutive isolates identified by partial 16S rRNA gene sequencing (26 isolates of the M. chelonae-M. abscessus complex and 64 remaining isolates, including Mycobacterium species, Nocardia species, and other aerobic actinomycetes) showed 100% specificity and sensitivity. The ITS PCR assay is accurate and specific, easy to perform, and a good supplemental test when using partial 16S rRNA gene sequencing to identify M. chelonae and M. abscessus.
Remote data checking using provable data possession

We introduce a model for provable data possession (PDP) that can be used for remote data checking: A client that has stored data at an untrusted server can verify that the server possesses the original data without retrieving it. The model generates probabilistic proofs of possession by sampling random sets of blocks from the server, which drastically reduces I/O costs. The client maintains a constant amount of metadata to verify the proof. The challenge/response protocol transmits a small, constant amount of data, which minimizes network communication. Thus, the PDP model for remote data checking is lightweight and supports large data sets in distributed storage systems. The model is also robust in that it incorporates mechanisms for mitigating arbitrary amounts of data corruption. We present two provably-secure PDP schemes that are more efficient than previous solutions. In particular, the overhead at the server is low (or even constant), as opposed to linear in the size of the data. We then propose a generic transformation that adds robustness to any remote data checking scheme based on spot checking. Experiments using our implementation verify the practicality of PDP and reveal that the performance of PDP is bounded by disk I/O and not by cryptographic computation. Finally, we conduct an in-depth experimental evaluation to study the tradeoffs in performance, security, and space overheads when adding robustness to a remote data checking scheme.
Association between the IL1B (-511), IL1B (+3954), IL1RN (VNTR) Polymorphisms and Graves' Disease Risk: A Meta-Analysis of 11 Case-Control Studies

Background Data on the association between the interleukin-1 (IL-1) gene polymorphisms and Graves' disease (GD) risk were conflicting. A meta-analysis was undertaken to assess this association. Methods We searched for case-control studies investigating the association between the IL1B (-511), IL1B (+3954), IL1RN (VNTR) polymorphisms and GD risk. We extracted data using standardized forms and calculated odds ratios (OR) with 95% confidence intervals (CI). Results A total of 11 case-control studies were included in this meta-analysis. Available data indicated that the IL1B (-511) polymorphism was associated with GD risk in the overall populations (Caucasians and Asians) in homozygote model (TT vs. CC, OR = 0.86, 95% CI: 0.76–0.97, Pz = 0.015), but not in dominant and recessive models (TT+TC vs. CC: OR = 0.95, 95% CI: 0.81–1.12, Pz = 0.553 and TT vs. TC+CC: OR = 0.82, 95% CI: 0.60–1.12, Pz = 0.205, respectively). No association between the IL1B (+3954), IL1RN (VNTR) polymorphisms and GD risk was found in the overall populations in any of the genetic models. In subgroup analyses according to ethnicity, the IL1B (-511) polymorphism was associated with GD risk in Asians in recessive and homozygote models (TT vs. TC+CC: OR = 0.68, 95% CI: 0.55–0.84, Pz<0.001 and TT vs. CC: OR = 0.81, 95% CI: 0.70–0.93, Pz = 0.003, respectively), but not in dominant model (TT+TC vs. CC: OR = 0.92, 95% CI: 0.77–1.11, Pz = 0.389). No association between the IL1B (+3954), IL1RN (VNTR) polymorphisms and GD risk was indicated in Asians, and we found no association between the IL1B (-511), IL1B (+3954), IL1RN (VNTR) polymorphisms and GD risk in Caucasians in any of the genetic models. Conclusion The IL1B (-511) polymorphism, but not the IL1B (+3954) and IL1RN (VNTR) polymorphisms was associated with GD risk in Asians. There was no association between these polymorphisms and GD risk in Caucasians.
Design of a filter against artifacts for JPEG2000

JPEG2000 Standard (ISO/IEC 15444, ITU-T T.800) is a new-generation image compression technique, enabling encoding images at low bit rates with acceptable quality. Since JPEG2000 is based on wavelet transforms, the reconstructed image will contain perceivable ringing artifacts in medium- and low-bit-rate regimes of lossy compression. We utilize a quad-tree partitioning scheme for postprocessing the reconstructed image in a spatially varying man- ner and presents a voting strategy to determine a set of morphologi- cal filters to be used for reducing the ringing artifacts. All this pro- cessing is performed at the encoder side, and the set of selected filters is conveyed to the decoder in the form of side information. Specifically, the adopted (eight) morphological filters are generated through the use of four predefined structuring elements (SEs) in conjunction with two morphological operations, namely, dilation and erosion. A voting strategy is used to select the morphological filter for each partition block to optimize the postprocessed image quality—through minimizing the sum of absolute differences under the constraint of a fixed quad-tree partition. Applying the chosen morphological filters to their corresponding blocks typically en- hances the reconstruction quality—in the worst case, leaving it un- changed. Simulation results demonstrate that the proposed tech- nique enhances reconstructed image quality compared to unprocessed JPEG2000 output at an equivalent bit rate, accounting for the side information overhead, in terms of both peak SNR (PSNR) and visible ringing measure (VRM). © 2005 SPIE and
Interactively Transferring CNN Patterns for Part Localization

In the scenario of one/multi-shot learning, conventional end-to-end learning strategies without sufficient supervision are usually not powerful enough to learn correct patterns from noisy signals. Thus, given a CNN pre-trained for object classification, this paper proposes a method that first summarizes the knowledge hidden inside the CNN into a dictionary of latent activation patterns, and then builds a new model for part localization by manually assembling latent patterns related to the target part via human interactions. We use very few (e.g., three) annotations of a semantic object part to retrieve certain latent patterns from conv-layers to represent the target part. We then visualize these latent patterns and ask users to further remove incorrect patterns, in order to refine part representation. With the guidance of human interactions, our method exhibited superior performance of part localization in experiments.
A new segmentation approach for handwritten digits

This article deals with a new segmentation approach applied to unconstrained handwritten digits. The novelty of the proposed algorithm is based on the combination of two types of structural features in order to provide the best segmentation path between connected entities. This method was developed to be applied in a segmentation-based recognition system. In this article, we first present the features used to generate our basic segmentation points. Then, we define our segmentation paths depending on the encountered configurations with only few heuristic rules. Finally, we evaluate the output of our segmenter using a neural network trained with isolated digits.
Design and Implementation of Semi-preemptible IO

Allowing higher-priority requests to preempt ongoing disk IOs is of particular benefit to delay-sensitive multimedia and real-time systems. In this paper we propose Semi-preemptible IO, which divides an IO request into small temporal units of disk commands to enable preemptible disk access. We present main design strategies to allow preemption of each component of a disk access--seek, rotation, and data transfer. We analyze the performance and describe implementation challenges. Our evaluation shows that Semi-preemptible IO can substantially reduce IO waiting time with little loss in disk throughput. For example, expected waiting time for disk IOs in a video streaming system is reduced 2.1 times with the throughput loss of less than 6 percent.
Lentiviral-Mediated RNA Interference against TGF-Beta Receptor Type II in Renal Epithelial and Fibroblast Cell Populations In Vitro Demonstrates Regulated Renal Fibrogenesis That Is More Efficient than a Nonlentiviral Vector

Background. Lentiviral constructs reportedly can integrate into the genome of non-dividing, terminally differentiated cells and dividing cells, for long-term gene expression. This investigation tested whether a third generation lentiviral-mediated small interfering RNA (siRNA) delivered into renal epithelial and fibroblast cells against type II transforming growth factor-beta receptor (siRNA-TBRII) could better attenuate renal fibrogenesis in comparison with a non-lentiviral construct. Methods. HIV-derived lentiviral and non-lentiviral constructs were used to transfect cells with siRNA-TBRII or siRNA-EGFP control. Human embryonic kidney (HEK-293T), renal epithelial cells (NRK-52E) and renal fibroblasts (NRK-49F) were transfected and gene silencing quantified (fluorescence microscopy, Western blotting, fluorescence-activated cell sorting). Renal fibrogenesis was assessed using extracellular matrix protein synthesis (fibronectin and collagen-III; Western immunoblot), and α-smooth muscle actin (α-SMA) was analysed as a marker of fibroblast activation and epithelial-to-mesenchymal transdifferentiation (EMT). Results. Lentiviral-mediated siRNA-TBRII significantly suppressed TBRII expression in all cell lines, and also significantly suppressed renal fibrogenesis. In comparison with the non-lentiviral construct, lentiviral-mediated siRNA-TBRII produced stronger and more persistent inhibition of collagen-III in NRK-49F cells, fibronectin in all renal cell lines, and α-SMA in renal epithelial cells. Conclusions. Lentiviral vector systems against TBRII can be delivered into renal cells to efficiently limit renal fibrogenesis by sequence-specific gene silencing.
On Coreferring Text-extracted Event Descriptions with the aid of Ontological Reasoning

Systems for automatic extraction of semantic information about events from large textual resources are now available: these tools are capable to generate RDF datasets about text extracted events and this knowledge can be used to reason over the recognized events. On the other hand, text based tasks for event recognition, as for example event coreference (i.e. recognizing whether two textual descriptions refer to the same event), do not take into account ontological information of the extracted events in their process. In this paper, we propose a method to derive event coreference on text extracted event data using semantic based rule reasoning. We demonstrate our method considering a limited (yet representative) set of event types: we introduce a formal analysis on their ontological properties and, on the base of this, we define a set of coreference criteria. We then implement these criteria as RDF-based reasoning rules to be applied on text extracted event data. We evaluate the effectiveness of our approach over a standard coreference benchmark dataset.
A Proposal for a Study on Treatment Selection and Lifestyle Recommendations in Chronic Inflammatory Diseases: A Danish Multidisciplinary Collaboration on Prognostic Factors and Personalised Medicine

Chronic inflammatory diseases (CIDs), including Crohn’s disease and ulcerative colitis (inflammatory bowel diseases, IBD), rheumatoid arthritis, psoriasis, psoriatic arthritis, spondyloarthritides, hidradenitis suppurativa, and immune-mediated uveitis, are treated with biologics targeting the pro-inflammatory molecule tumour necrosis factor-α (TNF) (i.e., TNF inhibitors). Approximately one-third of the patients do not respond to the treatment. Genetics and lifestyle may affect the treatment results. The aims of this multidisciplinary collaboration are to identify (1) molecular signatures of prognostic value to help tailor treatment decisions to an individual likely to initiate TNF inhibitor therapy, followed by (2) lifestyle factors that support achievement of optimised treatment outcome. This report describes the establishment of a cohort that aims to obtain this information. Clinical data including lifestyle and treatment response and biological specimens (blood, faeces, urine, and, in IBD patients, intestinal biopsies) are sampled prior to and while on TNF inhibitor therapy. Both hypothesis-driven and data-driven analyses will be performed according to pre-specified protocols including pathway analyses resulting from candidate gene expression analyses and global approaches (e.g., metabolomics, metagenomics, proteomics). The final purpose is to improve the lives of patients suffering from CIDs, by providing tools facilitating treatment selection and dietary recommendations likely to improve the clinical outcome.
Generic operating-system support for FPGAs

Field Programmable Gate Arrays (FPGAs) are by now common in industrial applications and research. The industry utilizes FPGAs for prototyping, small scale hardware productions, and telecommunication hardware. The deployment of FPGAs in research is often High Performance Computing (HPC) centric. But FPGAs are not used in General Purpose Computing (GPC) very often because of many factors, including missing Operating System (OS) support. This paper presents the idea of integrating FPGAs in OSs for standard personal computers, such as Linux, Mac OS X and Microsoft Windows. The goal of this integration is improving the acceptance of hardware acceleration for applications within software companies through separating hardware and software completely, and an easy hard- and software Application Programming Interface (API). Another goal is to improve the acceptance of FPGAs at the end-user by reducing the connection complexity of FPGAs and standard personal computers. The user should use them just by plug and play. To achieve these goals the paper introduces OS support for identifying and configuring FPGAs without vendor specific tools, and for bidirectional communication between the host computer and components configured inside the FPGA.
Permissive expansion and homing of adoptively transferred T cells in tumor‐bearing hosts

Activated T cells expressing endogenous or transduced TCRs are two cell types currently used in clinical adoptive T‐cell therapy. The ability of these cells to recognize their antigen, expand and traffic to the tumor site are the initial steps necessary for successful therapy. In this study, we used in vivo bioluminescent imaging (BLI) of Renilla luciferase (RLuc) expressing T cells to evaluate the ability of adoptively transferred T cells to survive, expand and home to tumor site in vivo. Using this method, termed RT‐Rack (Rluc T cell tracking), we followed T‐cell response against tumors in vivo. Expansion and homing of adoptively transferred T cells were antigen dependent, but independent of the host immune status. Moreover, we successfully detected T‐cell response to small and large tumors, including autochthonous liver tumors. The adoptively transferred T cells were not ignorant or excluded in a partially tolerant host, which expressed low level of the target in the periphery. Using T cell receptor (TCR)‐engineered T cells, we showed the ability of these cells to respond in tumor‐bearing hosts by expanding and homing to the tumor site. In all these models, the host immune status, the nature of the tumor or of the antigen, the tumor size and the presence of the targeted antigen in the periphery did not prevent the adoptively transferred T cells from responding by expanding and homing to the tumor. However, T cells had higher expression of the inhibitory receptor PD1 and reduced functional activity when a self‐antigen was targeted.
Contact Zone of Asian and European Wild Boar at North West of Iran

Wild boar (Sus scrofa) are widely distributed throughout the Old World. Most studies have focused on Europe and East Asia with the genetic diversity of West Asia being less well studied. In particular, the genetic variability and genetic structure of the Iranian populations are not yet known; gaps which prevent scientists from resolving the genetic relationships of the Eurasian wild boar. This paper is the first attempt to provide information about genetic relationships among modern Iranian populations of the Eurasian wild boar (S. scrofa) by sequencing 572 bp of the mitochondrial (mt) DNA control region. As a result of this investigation, it was discovered that Iran contains not only Middle Eastern haplotypes, but also shares haplotypes with Europe and East Asia. The Italian clade, which is endemic in Italy, is not identified in Iran, while all other clades, including Asiatic, European, Near East 1, and Near East 2 are found based on the phylogenetic tree and median-joining network. The results of this study illustrate that north west of Iran (specifically Southwest Caspian Sea) is the contact zone between the Asian (Near Eastern and Far Eastern), and the European clades. In light of the fact that the domestication of pigs occurs in Anatolia, this finding is important.
Robust computation of aggregates in wireless sensor networks: distributed randomized algorithms and analysis

A wireless sensor network consists of a large number of small, resource-constrained devices and usually operates in hostile environments that are prone to link and node failures. Computing aggregates such as average, minimum, maximum and sum is fundamental to various primitive functions of a sensor network like system monitoring, data querying, and collaborative information processing. In this paper we present and analyze a suite of randomized distributed algorithms to efficiently and robustly compute aggregates. Our distributed random grouping (DRG) algorithm is simple and natural and uses probabilistic grouping to progressively converge to the aggregate value. DRG is local and randomized and is naturally robust against dynamic topology changes from link/node failures. Although our algorithm is natural and simple, it is nontrivial to show that it converges to the correct aggregate value and to bound the time needed for convergence. Our analysis uses the eigen-structure of the underlying graph in a novel way to show convergence and to bound the running time of our algorithms. We also present simulation results of our algorithm and compare its performance to various other known distributed algorithms. Simulations show that DRG needs much less transmissions than other distributed localized schemes, namely gossip and broadcast flooding.