Miracle-dz/UniFAR-FTUs huggingface dataset:
Matrix Remodeling that Predict a Preferential Role of BRAF in Extracellular Thyroid Cells Is Associated with Gene Expression Profiles Conditional Activation of RET / PTC 3 and BRAFV 600 E in Updated

Papillary thyroid cancers (PTC) are associated with nonoverlapping mutations of genes coding for mitogen-activated protein kinase signaling effectors (i.e., the TK receptors RET or NTRK and the signaling proteins RAS and BRAF). We examined the pattern of gene expression after activation of these oncoproteins in thyroid PCCL3 cells, with the goal of identifying pathways or gene subsets that may account for the phenotypic differences observed in human cancers. We hybridized cDNA from cells treated with or without doxycycline to induce expression of BRAF, RET/PTC3, or RET/PTC3 with small interfering RNA–mediated knockdown of BRAF, respectively, to slides arrayed with a rat 70-mer oligonucleotide library consisting of 27,342 oligos. Among the RET/PTC3-induced genes, 2,552 did not require BRAF as they were similarly regulated by RET/PTC3 with or without BRAF knockdown and not by expression of BRAF. Immune response and IFN-related genes were highly represented in this group. About 24% of RET/PTC3-regulated genes were BRAF dependent, as they were similarly modified by RET/ PTC3 and BRAF but not in cells expressing RET/PTC3 with knockdown of BRAF. A gene cluster coding for components of the mitochondrial electron transport chain pathway was down-regulated in this group, potentially altering regulation of cell viability. Metalloproteinases were also preferentially induced by BRAF, particularly matrix metalloproteinase 3 (MMP3), MMP9, and MMP13. Accordingly, conditional expression of BRAF was associated with markedly increased invasion into Matrigel compared with cells expressing RET/PTC3. The preferential induction of MMPs by BRAF could explain in part the more invasive behavior of thyroid cancers with BRAF mutations. (Cancer Res 2006; 66(13): 6521-9)
Statistical Computing 2002 34 . Arbeitstagung über Methoden und Werkzeuge der Informatik für die Statistik Beiträge

The Heidelberg Retina Tomograph (HRT) provides topographic images of the optic nerve head by scanning the eye with a 670nm laser. As a precondition to medical analysis, the optic nerve head has to be outlined manually in clinical practise. Swindale et al. (2000) suggest automated classification of HRT images by a non-linear approximation of the image using the fitted parameters of a non-linear model. To evaluate the ability of this method to classify glaucomatous and normal eyes, we use a simulation model, which allows to create topography images of the optic nerve head in various forms (normal, glaucomatous and various progressive forms). We compare LDA, classification trees, bagging (Breiman, 1996), and bagging combined classifiers (Hothorn & Lausen, 2002). The methods are illustrated by data of a case control study (Mardin et al., 2002). We discuss possibilities for an improvement and optimization of image analysis for classification.
SeReCon: A Secure Dynamic Partial Reconfiguration Controller

As reconfigurable computing systems become more popular, concerns arise about their security and integrity. Runtime access to the configuration memory of dynamic partially reconfigurable FPGA devices offers new design possibilities, but also introduces security threats. This paper discusses various security threats present in such systems. The paper proposes a secure reconfiguration controller (SeReCon) which provides secure runtime management of designs downloaded to the DPR FPGA system and protects the design IP. SeReCon requires minor modification to the FPGA fabric. A prototype implementation of SeReCon is evaluated.
Design solutions for a low-power SoC platform using near-threshold voltages

In the future the number of small sensor-based devices is going to increase. The Internet-of-Everything (IoE) vision brings smart miniature electronic devices to objects surrounding our everyday lives. These devices are going to monitor our environment or ourselves. They are also going to execute small tasks based on their observations. Operations of this kind can be done with small low-performance devices. In this paper we present building blocks for a low-power system for sensor-based applications. Our work is aiming for reliable operation with supply voltage of 0.5 V instead of the nominal of 1.2 V. We describe low-power solutions used in 130 nm CMOS technology microprocessor, memory and clock generator. Depending on the component, we have managed to achieve reliable operation with voltages of 0.5-0.8 V. Power consumption of components reduce significantly when operating voltage is scaled down to near-threshold region.
Reimmunization after therapy for childhood cancer.

future. In the United Kingdom, ∼1600–1700 children aged ! 16 years receive diagnoses of cancer each year. Acute leukemia contributes to the most cases (approximately one-third of cases of childhood cancer), but many different types of childhood cancer are recognized. Intensive chemotherapy is a key component of treatment for almost all childhood malignancies, with surgery and/or radiotherapy required for selected patients. Some children with hematological malignancy in first remission, selected children with solid tumors in first remission, and many of those whose malignancy relapses will also undergo HSCT. Different malignancies require treatment with different chemotherapy drugs and schedules. However, risk stratification also plays an important role in planning treatment, with the intensity of the treatment tailored according to perceived risk on the basis of clinical and biological features of disease. Thus, not only do chemotherapy regimens vary for different diseases, but there may be significant variation in the intensity of the treatment regimen for patients with a single disease, depending on the risk group. HSCT procedures also vary in many ways. The cells that are used may come from bone marrow, cord blood, or peripheral blood. The donor may be the patient (autologous HSCT) or, for allogeneic HSCT, may be related or unrelated to the recipient and may be HLA-identical, wellmatched, mismatched, or haploidentical. Pretransplantation conditioning will usually involve cytotoxic drugs, but reducedintensity regimens are now used for some patients, and conditioning may or may not involve total body irradiation and T cell depletion. All of these factors may affect the rate of immune reconstitution after HSCT, as can the use of immunosuppressant agents, such as cyclosporin A, the presence of graft-versus-host disease, and the use of corticosteroids to control graftversus-host disease. The myelosuppressive effects of intensive chemotherapy and the immunosuppression that arises from the use of oral continuation chemotherapy with corticosteroids in acute lymphoblastic leukemia are well recognized. Immunosuppression and the risk of infection gradually resolve over a period of some months after the discontinuation of treatment, although the time course is not well documented. After HSCT, the risk of infection is even greater and continues during a prolonged period of immune reconstitution, which may be affected by many factors. For example, children who have received total body irradiation are perceived to be at indefinite risk of infection with pneumococcus.
Human Resource Flexibility and Organizational Effectiveness: Role of Organizational Citizenship Behaviour and Employee Intent to Stay

Purpose: Human resource flexibility is an important domain of study in organizational research. 21 st century organizations require a flexible system in its portfolio, which should encourage employees to be evolved with multiple job skills and abilities to sustain in the face of competitive result driven environment. In this context the purpose of the present paper is to develop a comprehensive theoretical framework to examine the interrelationship between human resource flexibility and organizational effectiveness. Further, it tries to establish the possible role of organizational citizenship behavior and employee intent to stay on the relationship between human resource flexibility and organizational effectiveness. Design / Methodology/ Approach: The paper follows the method of in-depth and extant literature survey to critically examine and rationalize the influence of human resource flexibility on organizational effectiveness for Indian organizations. Conclusions/Findings: The review provides a comprehensive theoretical framework to develop a conceptual model of human resource flexibility. The proposed model includes human resource flexibility, dimensions of organizational effectiveness, organizational citizenship behavior, and employee intent to stay. Research and Practical Implications: The theoretical framework proposed in this paper on HR flexibility would help researchers and management expert to understand the role of HR flexibility in producing better results for business organizations. This paper has a number of implications for HR Practitioners and management experts which could be utilized to nurture good HR flexibility in its system for better performance of the employees as well as of the organization. Original Contribution: The study contributes towards the broader understanding of the construct of HR flexibility and proposes a new theoretical model in the Indian context.
Word candidate generation in Cyrillic OCR based on ALN classifiers

The process of recognizing characters from a scanned image can be divided into three main operational steps: document layout analysis, character recognition, and contextual postprocessing. This paper addresses the step of contextual postprocessing using the extended information received from the pattern classifiers as well as the information about the pattern preclassification according to its shape. Every pattern is examined by several classifiers, and their decisions are combined in a list of character candidates along with their levels of confidence. Combining the character candidates on different letter positions generates a list of word candidates and the lexicon is being checked for their existence. Word candidates are generated one at a time, in sequence of descending word confidence, and the first candidate found in the lexicon is accepted.
On the use of likelihood ratio and GNC for the restoration of SAR images

Several methods have already been developped in order to solve the problem of restoring blurred images corrupted by gaussian noise. Our goal is here to adapt these methods to synthetic aperture radar (SAR) images. This kind of images has particular properties that we describe below. Modifications to the methods are then suggested. The choice of the algorithm allowing the computation of the smoothed image is discussed. Some results on simulated and real images are then presented.
High Confidence Software Environments for Embedded Control Systems Design

We propose the development of a software environment for design of real-time, control systems that generates validated, embedded software for use as part of the open control platform. This environment will include languages for specifying desired performance of the system, translation tools for converting these performance specifications into control specifications in a semi-automated fashion, and verification tools that allow the (hybrid) control algorithms to be validated against the specification in a way that describes the conditions required for successful execution. We plan to build this environment on top of the existing software tools that are being developed at Caltech for real-time, optimization based control, as well as the open control platform. A novel feature of the software environment will be that the control specification will support dynamic reconfiguration to accommodate changes in mission, condition, and external environment. Our work will center on the use of mathematical approaches to develop a prototype framework for high confidence systems that will explore the use of such tools in the context of a specific example system. In particular, we will study the problem of controlling a small flock of unmanned vehicles performing a coordinated task in the presence of adversaries. We will assume that vehicles fail and such failures should be accommodated by the software system. This class of problems is representative of many problems of importance to the DoD and will push the toolset to consider problems of DoD relevance. The software developed under this program will generate embedded code that is compatible with the open control platform currently under development as part of the Software Enabled Control program. To further demonstrate the applicability of our approach, we will implement the control laws and demonstrate their performance on a hardware platform that is being developed at Caltech. This platform consists of two sets of 4-5 vehicles each that can communicate via a variety of different protocols. Failures in connections between vehicles will be simulated to test the robustness of the proposed approach. Each node in this distributed system will be capable of executing model-predictive control laws with online-control customization through modification of the performance objective and (active-state) vehicle and environmental models. The vehicle and flock management levels of the control will use the code generated by the software environment to tie together the distributed computations of the individual vehicles.
Assembly-Based Method Engineering with Method Patterns

Software development methods prescribe and coordinate the activities necessary to plan, build, and deliver software. To provide methods that account for the situational context of a development project, e.g., an acquirer-supplierrelationship or specific communication needs, the existing method creation approaches represent a trade-off between flexibility and ease of use. On the one side, less flexible configurable methods offer a fixed set of configurations to quickly adapt a method to the situation at hand. On the other side, assembly-based approaches allow creating methods from scratch by combining preexisting building blocks. Thus, they are more flexible and capable of creating methods not covered by configurations of configurable methods, e.g., a mixture of agile and plan-driven ideas. However, assembly-based approaches are not easy to use and require considerable expert knowledge. In this paper we suggest the use of method patterns during the assembly-based method creation. Method patterns represent desirable principles for the to-be-method and therefore support the right choice and combination of method building blocks, simplifying assembly-based method creation.
Under Consideration for Publication in Theory and Practice of Logic Programming on Cascade Products of Answer Set Programs

Describing complex objects by elementary ones is a common strategy in mathematics and science in general. In their seminal 1965 paper, Kenneth Krohn and John Rhodes showed that every finite deterministic automaton can be represented (or " emulated ") by a cascade product of very simple automata. This led to an elegant algebraic theory of automata based on finite semigroups (Krohn-Rhodes Theory). Surprisingly, by relating logic programs and automata, we can show in this paper that the Krohn-Rhodes Theory is applicable in Answer Set Programming (ASP). More precisely, we recast the concept of a cascade product to ASP, and prove that every program can be represented by a product of very simple programs, the reset and standard programs. Roughly, this implies that the reset and standard programs are the basic building blocks of ASP with respect to the cascade product. In a broader sense, this paper is a first step towards an algebraic theory of products and networks of nonmonotonic reasoning systems based on Krohn-Rhodes Theory, aiming at important open issues in ASP and AI in general.
BiGUL: a formally verified core language for putback-based bidirectional programming

Putback-based bidirectional programming allows the programmer to write only one putback transformation, from which the unique corresponding forward transformation is derived for free. The logic of a putback transformation is more sophisticated than that of a forward transformation and does not always give rise to well-behaved bidirectional programs; this calls for more robust language design to support development of well-behaved putback transformations. In this paper, we design and implement a concise core language BiGUL for putback-based bidirectional programming to serve as a foundation for higher-level putback-based languages. BiGUL is completely formally verified in the dependently typed programming language Agda to guarantee that any putback transformation written in BiGUL is well-behaved.
A New Class of Highly Fault Tolerant Erasure Code for the Disk Array

We present a new class of erasure codes of size ntimesn (n is a prime number) called T-code, a new family of simple, highly fault tolerant XOR-based erasure codes for storage systems (with fault tolerance up to 15). T-code is not maximum distance separable (MDS), but has many other advantages, such as high fault tolerance, simple computability, and high efficiency of coding and decoding. Because of its superior quantity over many other erasure codes for the storage system, this new coding technology is more suited in RAID or dRAID systems.
[The endoscopic diagnosis and therapy as well as the long-term course of Dieulafoy ulcer hemorrhage].

OBJECTIVE To assess the effectiveness of endoscopic diagnosis and treatment as well as the long-term course in patients with bleeding from Dieulafoy's ulcer (DU). PATIENTS AND METHODS Data were gathered on all cases coded "bleeding from Dieulafoy's ulcer" in an endoscopic data-bank. The following items were obtained from the case-notes: clinical symptoms, mean haemoglobin concentration, demand for infusion of erythrocyte concentrates and endoscopic procedures undertaken for diagnosis and treatment. There were 15 patients (mean age 64.8 years; 9 men and 6 women), seen between 1985 and 1998 with the diagnosis of DU. All lesions were located in the proximal stomach. The effectiveness of the various parameters was analysed. The long-term course was ascertained by telephone interviews with the patients and (or) their general practitioner. RESULTS The suspected diagnosis of DU was confirmed by additional endoscopic means such as endoscopic Doppler sonography or endosonography. A combination of endoscopic techniques of stopping the bleeding (epinephrine injection and, if necessary, haemoclip application) was effective in 14 of the 15 patients, operative intervention being required in one. Three patients died during follow-up, none of bleeding. No recurrence of bleeding had occurred in the 10 patients followed for a mean of 20 (6-31) months. CONCLUSIONS The endoscopic diagnosis of DU bleeding can be confirmed by endoscopic Doppler sonography or endosonography. It remains to be proven whether miniscope endosonography is of additional value. The combined method of stopping the bleeding has been effective in this patient collective, both during hospitalization and on long-term follow-up.
The Teaching Alliance Inventory: Evaluating the student-instructor relationship in clinical and counselling psychology training

The Teaching Alliance Inventory (TAI) was developed to measure the quality of the student-instructor relationship in graduate clinical and counselling psychology classrooms. Based on Bordin's (1983) original concept of the alliance as fundamental to the change process in psychotherapy, we developed the TAI to measure aspects of the classroom relationship that may be fundamental to learning essential skills of counselling and clinical psychology. Factor analysis revealed six subscales, four representing interpersonal variables not evaluated in traditional teaching effectiveness measures. We demonstrated internal consistency and split-half reliability with a large sample of graduate students and described evidence for the scale's face validity and content validity. Construct validity was supported by significant correlations between the TAI and its subscales with an established measure of teaching effectives and its logically related subscales (SEEQ; Marsh, 1987). The TAI may supplement traditional assessments of instructor quality by providing feedback regarding interpersonal impact in the classroom.
What do we know about the transient receptor potential vanilloid 2 (TRPV2) ion channel?

Transient receptor potential (TRP) ion channels are emerging as a new set of membrane proteins involved in a vast array of cellular processes and regulated by a large number of physical and chemical stimuli, which involves them with sensory cell physiology. The vanilloid TRP subfamily (TRPV) named after the vanilloid receptor 1 (TRPV1) consists of six members, and at least four of them (TRPV1–TRPV4) have been related to thermal sensation. One of the least characterized members of the TRP subfamily is TRPV2. Although initially characterized as a noxious heat sensor, TRPV2 now seems to have little to do with temperature sensing but a much more complex physiological profile. Here we review the available information and research progress on the structure, physiology and pharmacology of TRPV2 in an attempt to shed some light on the physiological and pharmacological deorphanization of TRPV2.
Trypanosoma cruzi heparin-binding proteins mediate the adherence of epimastigotes to the midgut epithelial cells of Rhodnius prolixus

SUMMARY Heparin-binding proteins (HBPs) have been demonstrated in both infective forms of Trypanosoma cruzi and are involved in the recognition and invasion of mammalian cells. In this study, we evaluated the potential biological function of these proteins during the parasite-vector interaction. HBPs, with molecular masses of 65·8 kDa and 59 kDa, were isolated from epimastigotes by heparin affinity chromatography and identified by biotin-conjugated sulfated glycosaminoglycans (GAGs). Surface plasmon resonance biosensor analysis demonstrated stable receptor-ligand binding based on the association and dissociation values. Pre-incubation of epimastigotes with GAGs led to an inhibition of parasite binding to immobilized heparin. Competition assays were performed to evaluate the role of the HBP-GAG interaction in the recognition and adhesion of epimastigotes to midgut epithelial cells of Rhodnius prolixus. Epithelial cells pre-incubated with HBPs yielded a 3·8-fold inhibition in the adhesion of epimastigotes. The pre-treatment of epimastigotes with heparin, heparan sulfate and chondroitin sulfate significantly inhibited parasite adhesion to midgut epithelial cells, which was confirmed by scanning electron microscopy. We provide evidence that heparin-binding proteins are found on the surface of T. cruzi epimastigotes and demonstrate their key role in the recognition of sulfated GAGs on the surface of midgut epithelial cells of the insect vector.