Miracle-dz/UniFAR-FTUs huggingface dataset:
Sinonasal inverted papilloma associated with squamous cell carcinoma

Sinonasal inverted papilloma associated with squamous cell carcinoma Background. The aims of the study were to review single-institution experiences with sinonasal inverted papilloma associated with squamous cell carcinoma (IP/SCC), to analyze the presence of human papillomavirus (HPV) and to evaluate the role of radiotherapy. Patients and methods. Five patients with IP/SCC were identified in the prospective institutional databases (1995-2005) and HPV status was determined in all five tumors. Results. Four out of five patients had T3-4 tumors; no nodal involvement was seen in any of them. Four patients had curative surgery, supplemented in three of them with radiotherapy. Debulking surgery was performed in the patient with a non-resectable tumor followed by radical radiotherapy. Tumor was controlled locally in three patients at 8, 46 and 58 months post-surgery. Local failure occurred in two patients: after endoscopic resection of a T1 tumor (the recurrent tumor was successfully salvaged with additional surgery) and in a patient with an inoperable tumor. No regional or distant metastases occurred. HPV status was determined in all five tumors and three of them were found positive for HPV type 11. Conclusions. In operable sinonasal IP/SCC, upfront surgery and postoperative radiotherapy to the tumor bed with dose levels comparable to those used for invasive SCC are recommended. For non-resectable disease, radical radiotherapy to a dose of 66-70 Gy could be of benefit.
Foveal Word Reading Requires Interhemispheric Communication

The left cerebral hemisphere is dominant for language processing in most individuals. It has been suggested that this asymmetric language representation can influence behavioral performance in foveal word-naming tasks. We carried out two experiments in which we obtained laterality indices by means of functional imaging during a mental word-generation task, using functional transcranial Doppler sonography and functional magnetic resonance imaging, respectively. Subsequently, we administered a behavioral word-naming task, where participants had to name foveally presented words of different lengths shown in different fixation locations shifted horizontally across the screen. The optimal viewing position for left language dominant individuals is located between the beginning and the center of a word. It is shifted toward the end of a word for right language dominant individuals and, to a lesser extent, for individuals with bilateral language representation. These results demonstrate that interhemispheric communication is required for foveal word recognition. Consequently, asymmetric representations of language and processes of interhemispheric transfer should be taken into account in theoretical models of visual word recognition to ensure neurological plausibility.
Synaptic repair mechanisms responsible for functional recovery in various cochlear pathologies.

In some cochlear pathologies, temporary hearing loss can be followed by complete or partial functional recovery. Our previous findings suggest the involvement of an excitotoxic (glutamate-related) disruption of inner hair cell (IHC)-auditory nerve synapses, followed by synaptic regeneration. It is essential to understand the molecular mechanisms responsible for this synaptic repair if new therapeutic strategies are to be developed. In guinea pig cochleas, acute synaptic excitotoxic damage (mimicking what occurs with acoustic trauma or local ischemia) is achieved by locally applying AMPA, a glutamate agonist. This results in a total disruption of all IHC-auditory dendrite synapses, together with a disappearance of cochlear potentials. Within the next 5 days, however, a recovery of both the normal pattern of IHC innervation and the physiological responses is observed. The fact that the blockage of the NMDA receptors during functional recovery delayed the regrowth of neurites and the restoration of hearing suggests that glutamate plays a neurotrophic role via activation of NMDA receptors. Experiments are in progress to investigate, among other factors, the role of other glutamate receptor subunits. A reversible in vivo antisense strategy is being developed to overcome the lack of specificity of some antagonists. First results bode well for future pharmacological therapies in cochlear pathologies where glutamatergic synapses are likely to be involved; i.e., noise trauma, ischemia-related sudden deafness, and neural presbycusis.
Evaluating an embedded software reference architecture - industrial experience report

In this paper, we discuss experiences gained during evaluation of the maintainability of a reference architecture in use at Oce, one of the world's leading copier manufacturers. The evaluation is conducted using an approach based on SEI's software architecture analysis method (SAAM). The paper proposes a variant of SAAM that helps to reduce the organisational impact of architecture evaluations. Second, we analyse the implications of evaluating reference architectures as opposed to single-product architectures. Furthermore, we share our experience of conducting the evaluation, draw lessons for practitioners, and propose new research topics.
External quality assessment unravels interlaboratory differences in quality of RAS testing for anti-EGFR therapy in colorectal cancer.

BACKGROUND Regulations for the selection of patients with metastatic colorectal cancer for anti-EGFR treatment changed at the end of 2013. The set of mutations to be tested extended from KRAS codons 12 and 13 to KRAS and NRAS exons 2, 3, and 4. A European external quality assessment scheme monitored the performance of laboratories and evaluated the implementation of the new regulations. MATERIALS AND METHODS The 131 participating laboratories received 10 samples of formalin-fixed paraffin-embedded material, including RAS (exon 2, 3, 4) and BRAF mutations. Mock clinical data were provided for three cases. Using their routine methods, laboratories determined the genotypes and submitted three written reports. Assessors scored the results according to predefined evaluation criteria. RESULTS Half of the participants (49.3%) had completely implemented the new test requirements (codons 12, 13, 59, 61, 117, and 146 of KRAS and NRAS), and 96 laboratories (73.3%) made no genotype mistakes. Correct nomenclature, according to the Human Genome Variation Society, was used by 82 laboratories (62.6%). CONCLUSION Although regulations were effective for several months, many laboratories were not ready for full RAS testing in the context of anti-EGFR therapy. Nevertheless, in each participating country, there are laboratories that provide complete and correct testing. External quality assessments can be used to monitor implementation of new test regulations and to stimulate the laboratories to improve their testing procedures. Because the results of this program are available on the website of the European Society of Pathology, patients and clinicians can refer test samples to a reliable laboratory.
OBJCUT: Efficient Segmentation Using Top-Down and Bottom-Up Cues

We present a probabilistic method for segmenting instances of a particular object category within an image. Our approach overcomes the deficiencies of previous segmentation techniques based on traditional grid conditional random fields (CRF), namely that 1) they require the user to provide seed pixels for the foreground and the background and 2) they provide a poor prior for specific shapes due to the small neighborhood size of grid CRF. Specifically, we automatically obtain the pose of the object in a given image instead of relying on manual interaction. Furthermore, we employ a probabilistic model which includes shape potentials for the object to incorporate top-down information that is global across the image, in addition to the grid clique potentials which provide the bottom-up information used in previous approaches. The shape potentials are provided by the pose of the object obtained using an object category model. We represent articulated object categories using a novel layered pictorial structures model. Nonarticulated object categories are modeled using a set of exemplars. These object category models have the advantage that they can handle large intraclass shape, appearance, and spatial variation. We develop an efficient method, OBJCUT, to obtain segmentations using our probabilistic framework. Novel aspects of this method include: 1) efficient algorithms for sampling the object category models of our choice and 2) the observation that a sampling-based approximation of the expected log-likelihood of the model can be increased by a single graph cut. Results are presented on several articulated (e.g., animals) and nonarticulated (e.g., fruits) object categories. We provide a favorable comparison of our method with the state of the art in object category specific image segmentation, specifically the methods of Leibe and Schiele and Schoenemann and Cremers.
Firewood and timber exploitation during the third and second millennia BC in Northwestern Iberia: wood resources, territories and chaîne opératoire

This research was developed under the projects: Forest and scrubland management from Iron Age to roman period in the northwest of the Iberian Peninsula: firewood consumption and wooden manufacture production; IDEPatri ‑Design and development of a data model for an archaeological SPI during the Galician Iron Age – 09SEC002CT; Bronze Age Landscapes in the West of Iberian Peninsula – SFRH/BSAB/986/10 and Geoindicators of natural and anthropogenic palaeoenvironmental evolution in the Portuguese NW, during de Holocene – 2010/CGUP/CCT/UM.
Examination of clinical and environmental Vibrio parahaemolyticus isolates by multi-locus sequence typing (MLST) and multiple-locus variable-number tandem-repeat analysis (MLVA)

Vibrio parahaemolyticus is a leading cause of seafood-borne infections in the US. This organism has a high genetic diversity that complicates identification of strain relatedness and epidemiological investigations. However, sequence-based analysis methods are promising tools for these identifications. In this study, Multi-Locus Sequence Typing (MLST) and Multiple-Locus Variable-Number Tandem-Repeat Analysis (MLVA) was performed on 58 V. parahaemolyticus isolates (28 of oyster and 30 of clinical origin), to identify differences in phylogeny. The results obtained by both methods were compared to Pulsed-Field Gel Electrophoresis (PFGE) patterns determined in a previous study. Forty-one unique sequence types (STs) were identified by MLST among the 58 isolates. Almost half of the isolates (22) belonged to a new ST and added to the MLST database. A ST could not be generated for 5 (8.6%) isolates, primarily due to an untypable recA locus. Analysis with eBURST did not identify any clonal complex among the strains analyzed and revealed 37 singeltons with 4 of them forming 2 groups (1 of them SLV, and the other a DLV). An established MLVA assay, targeting 12 total genes through three separate 4-plex PCRs, was successfully adapted to high resolution melt (HRM) analysis with faster and easier experimental setup; resulting in 58 unique melt curve patterns. HRM-MLVA was capable of differentiating isolates within the same PFGE cluster and having the same ST. Conclusively, combining the three methods PFGE, MLST, and HRM-MLVA, for the phylogenetic analysis of V. parahaemolyticus resulted in a high resolution subtyping scheme for V. parahaemolyticus. This scheme will be useful as a phylogenetic research tool and as an improved method for outbreak investigations for V. parahaemolyticus.
Evidence for the use of probiotics and prebiotics in inflammatory bowel disease: a review of clinical trials

Human subjects and their enteric microbiota have evolved together to reach a state of mutual tolerance. Mounting evidence from both animal models and human studies suggests that inflammatory bowel disease (IBD) represents a malfunction of this relationship. The enteric microecology therefore represents an attractive therapeutic target with few side effects. Probiotics and prebiotics have been investigated in clinical trials as treatments for IBD, with conflicting results. The evidence for the use of probiotics in the management of pouchitis is persuasive and several studies indicate their effectiveness in ulcerative colitis. Trials of probiotics and prebiotics in Crohn's disease are less convincing. However, methodologies vary widely and a range of probiotic, prebiotic and combination (synbiotic) treatments have been tested in a variety of patient groups with an assortment of end points. Conclusions about any one treatment in a specific patient group can therefore only be drawn on evidence from relatively small numbers of patients. The present article reviews the role of the intestinal microbiota in the pathogenesis of IBD and addresses the clinical evidence for the therapeutic manipulation of bowel microbiota using probiotics, prebiotics and synbiotics in IBD.
A Self-Stabilizing Locality-Aware Peer-to-Peer Network Combining Random Networks, Search Trees, and DHTs

We present 3nuts, a self-stabilizing peer-to-peer (p2p) network supporting range queries and adapting the overlay structure to the underlying physical network. 3nuts combines concepts of structured and unstructured p2p networks to over-come their individual shortcomings while keeping their strengths. This is achieved by combining self maintaining random networks for robustness, a search tree to allow range queries, and DHTs for load balancing. Simple handshake operations with provable guarantees are used for maintenance and self-stabilization. Efficiency of load balancing, fast data access, and robustness are proven by rigorous analysis.
Simultaneous learning of a discriminative projection and prototypes for Nearest-Neighbor classification

Computer vision and image recognition research have a great interest in dimensionality reduction techniques. Generally these techniques are independent of the classifier being used and the learning of the classifier is carried out after the dimensionality reduction is performed, possibly discarding valuable information. In this paper we propose an iterative algorithm that simultaneously learns a linear projection base and a reduced set of prototypes optimized for the Nearest-Neighbor classifier. The algorithm is derived by minimizing a suitable estimation of the classification error probability. The proposed approach is assessed through a series of experiments showing a good behavior and a real potential for practical applications.
A Distributed Processing Communication Scheme for Real-Time Applications over Wide-Area Networks

Low-delay networking and edge computing will enable mission-critical applications to be delivered over wide-area networks. We consider this trend to be the realization that all users can share an application space without feeling any distance difference. We propose a distributed processing scheme that keeps the order of event occurrence regardless of the distance between users and an application server. The proposed scheme can be applied to both optimistic synchronization algorithms (OSA) and conservative synchronization algorithms (CSA). In the proposed scheme, arrival events with a delay within a predefined set time (correction time) are sorted in order of occurrence before application processing. We formulate the proposed scheme as an integer linear programming (ILP) problem. The objective function of ILP consists of the number of users excluded from the delay quality, the amount of memory consumed for a rollback in OSA, and the maximum end-to-end delay. The three parts of the objective function are set weight and the sum of parts with weight is minimized. We evaluate the proposed scheme for 1000 users distributed in two types of network models. Numerical results indicate that the proposed scheme reduces memory consumption compared to that of the conventional OSA scheme. The proposed scheme works as CSA in which all events are sorted in the occurrence order if the correction time is set above the delay for the slowest event to arrive at the server.
Intermediate Filaments Play a Pivotal Role in Regulating Cell Architecture and Function*

Intermediate filaments (IFs) are composed of one or more members of a large family of cytoskeletal proteins, whose expression is cell- and tissue type-specific. Their importance in regulating the physiological properties of cells is becoming widely recognized in functions ranging from cell motility to signal transduction. IF proteins assemble into nanoscale biopolymers with unique strain-hardening properties that are related to their roles in regulating the mechanical integrity of cells. Furthermore, mutations in the genes encoding IF proteins cause a wide range of human diseases. Due to the number of different types of IF proteins, we have limited this short review to cover structure and function topics mainly related to the simpler homopolymeric IF networks composed of vimentin, and specifically for diseases, the related muscle-specific desmin IF networks.
The effect of the GENTLE/s robot-mediated therapy system on arm function after stroke

Objective: To evaluate the effect of robot-mediated therapy on arm dysfunction post stroke. Design: A series of single-case studies using a randomized multiple baseline design with ABC or ACB order. Subjects (n = 20) had a baseline length of 8, 9 or 10 data points. They continued measurement during the B — robot-mediated therapy and C — sling suspension phases. Setting: Physiotherapy department, teaching hospital. Subjects: Twenty subjects with varying degrees of motor and sensory deficit completed the study. Subjects attended three times a week, with each phase lasting three weeks. Interventions: In the robot-mediated therapy phase they practised three functional exercises with haptic and visual feedback from the system. In the sling suspension phase they practised three single-plane exercises. Each treatment phase was three weeks long. Main measures: The range of active shoulder flexion, the Fugl-Meyer motor assessment and the Motor Assessment Scale were measured at each visit. Results: Each subject had a varied response to the measurement and intervention phases. The rate of recovery was greater during the robot-mediated therapy phase than in the baseline phase for the majority of subjects. The rate of recovery during the robot-mediated therapy phase was also greater than that during the sling suspension phase for most subjects. Conclusion: The positive treatment effect for both groups suggests that robot-mediated therapy can have a treatment effect greater than the same duration of non-functional exercises. Further studies investigating the optimal duration of treatment in the form of a randomized controlled trial are warranted.
Regulation of muscle differentiation: stimulation of myoblast fusion in vitro by catecholamines.

Epinephrine and isoproterenol provoke primary chick myoblasts to initiate precocious cell fusion. Both the rise in intracellular adenosine 3' ,5-monophosphate (cyclic AMP) and cell fusion generated by these effectors are prevented by propranolol, which is a specific blocker of the beta-adrenergic receptor. Propranolol has no effect either on the precocious cell fusion provoked by prostaglandin E or on cell fusion in control cultures. The results support the idea that a rise in cyclic AMP is the critical intracellular change responsible for initiating events that culminate in myoblast differentiation 4 to 5 hours later. They also indicate that the culminate in myoblast differentiation 4 to 5 hours later. They also indicate that the hormone responsible for the positive regulation of myoblast differentiation in vitro is not acting through the beta-adrenergic receptor.
Water Use and Yield of Soybean under Various Irrigation Regimes and Severe Water Stress. Application of AquaCrop and SIMDualKc Models

Data relative to two soybean seasons, several irrigation scheduling treatments, including moderate and severe deficit irrigation, and rain-fed cropping were used to parameterize and assess the performance of models AquaCrop and SIMDualKc, the latter combined with the Stewart’s yield model. SIMDualKc applies the FAO56 dual crop coefficient approach for computing and partitioning evapotranspiration (ET) into actual crop transpiration (Tc act) and soil evaporation (Es), while AquaCrop uses an approach that depends on the canopy cover curve. The calibration-validations of models were performed by comparing observed and predicted soil water content (SWC) and grain yield. SIMDualKc showed good accuracy for SWC estimations, with normalized root mean square error (NRMSE) ≤ 7.6%. AquaCrop was less accurate, with NRMSE ≤ 9.2%. Differences between models regarding the water balance terms were notable, and the ET partition revealed a trend for under-estimation of Tc act by AquaCrop, mainly under severe water stress. Yield predictions with SIMDualKc-Stewart models produced NRMSE < 15% while predictions with AquaCrop resulted in NRMSE ≤ 23% due to under-estimation of Tc act, particularly for water stressed treatments. Results show the appropriateness of SIMDualKc to support irrigation scheduling and assessing impacts on yield when combined with Stewart’s model.
Sentence-Internal Prosody Does not Help Parsing the Way Punctuation Does

This paper investigates the usefulness of sentence-internal prosodic cues in syntactic parsing of transcribed speech. Intu-itively, prosodic cues would seem to provide much the same information in speech as punctuation does in text, so we tried to incorporate them into our parser in much the same way as punctuation is. We compared the accuracy of a statistical parser on the LDC Switchboard treebank corpus of transcribed sentence-segmented speech using various combinations of punctuation and sentence-internal prosodic information (duration, pausing, and f0 cues). With no prosodic or punctuation information the parser’s accuracy (as measured by F-score) is 86.9%, and adding punctuation increases its F-score to 88.2%. However, all of the ways we have tried of adding prosodic information decrease the parser’s F-score to between 84.8% to 86.8%, depending on exactly which prosodic information is added. This suggests that for sentence-internal prosodic information to improve speech transcript parsing, either different prosodic cues will have to used or they will have be exploited in the parser in a way different to that used currently.
Nuclear positioning rather than contraction controls ordered rearrangements of immunoglobulin loci

Progenitor-B cells recombine their immunoglobulin (Ig) loci to create unique antigen receptors. Despite a common recombination machinery, the Ig heavy and Ig light chain loci rearrange in a stepwise manner. We studied pre-pro-B cells and Rag−/− progenitor-B cells to determine whether Ig locus contraction or nuclear positioning is decisive for stepwise rearrangements. We found that both Ig loci were contracted in pro-B and pre-B cells. Igh relocated from the nuclear lamina to central domains only at the pro-B cell stage, whereas, Igκ remained sequestered at the lamina, and only at the pre-B cell stage located to central nuclear domains. Finally, in vitro induced re-positioning of Ig alleles away from the nuclear periphery increased germline transcription of Ig loci in pre-pro-B cells. Thus, Ig locus contraction juxtaposes genomically distant elements to mediate efficient recombination, however, sequential positioning of Ig loci away from the nuclear periphery determines stage-specific accessibility of Ig loci.