Miracle-dz/UniFAR-FTUs huggingface dataset:
Center Determination for Cone-Beam X-ray Tomography

In order to render 3D model of the bone, the stack of cross-sectional images must be reconstructed from a series of X-ray radiographs, served as the projections. In the case where the distance between x-ray source and detector is not infinite, image reconstruction from projection based on parallel-beam geometry provides an error in the cross-sectional image. In such case, image reconstruction from projection based on conebeam geometry must be exercised instead. This paper is devoted to the determination of detector center for SART conebeam Technique which is critically effect the performance of the resulting 3D modeling.
Allogeneic bone marrow transplantation with T‐cell‐depleted marrow grafts for patients with poor‐risk relapsed low‐grade non‐Hodgkin's lymphoma

We present the clinical results of allogeneic bone marrow transplantation (BMT) with T‐cell‐depleted grafts from HLA‐matched sibling donors in patients with poor‐risk relapsed low‐grade non‐Hodgkin's lymphoma (NHL). Poor risk was defined as relapse within 12 months after or progression during prior treatment. The conditioning regimen consisted of cyclophosphamide and total‐body irradiation with or without additional idarubicin. Donor marrow was depleted of T lymphocytes using counterflow centrifugation. Post‐BMT prophylaxis of graft‐versus‐host disease (GvHD) consisted of cyclosporine A. 15 patients with a median age of 47 years (range 30–57) were transplanted. All patients engrafted. After a median follow‐up of 36 months (range 9–78), 10 patients were alive and in complete remission (CR). Two of them had relapsed after BMT but re‐entered CR following infusions of leucocytes from the original bone marrow donor. Five patients died; causes of death were cardiomyopathy (n = 1), chronic GvHD (n = 1) and infection during chronic GvHD (n = 3). We conclude that allogeneic T‐cell‐depleted bone marrow transplantation is an efficacious treatment for patients with poor‐risk relapsed low‐grade NHL. Infusions of donor leucocytes reinduced CR in the two patients with relapse after BMT.
Cortical asymmetry in Parkinson's disease: early susceptibility of the left hemisphere

Clinically, Parkinson's disease (PD) presents with asymmetric motor symptoms. The left nigrostriatal system appears more susceptible to early degeneration than the right, and a left‐lateralized pattern of early neuropathological changes is also described in several neurodegenerative conditions, including Alzheimer's disease, frontotemporal dementia, and Huntington's disease. In this study, we evaluated hemispheric differences in estimated rates of atrophy in a large, well‐characterized cohort of PD patients.
Application of the World Health Organization system for HIV infection in a cohort of homosexual men in developing a prognostically meaningful staging system

ObjectiveValidation of a modified version of the recently proposed World Health Organization (WHO) staging system for HIV infection and disease in a cohort of homosexual men. MethodsFive hundred and thirty HIV-positive men followed for a median of 51 months (range, 1–98 months) were eligible for analysis. Subjects were classified into stages at their first seropositive visit and at all subsequent visits. ResultsAs of 1 April 1991, 136 subjects (26%) had progressed to stage IV of the modified WHO system on the basis of their CD4 lymphocyte counts, and 78 subjects (15%) had died. Kaplan-Meier estimates for progression to stage IV from stages I, II and III were 52.8 ± 7.5% over 6.6 years, 58.1 ± 7.1% over 5.9 years and 66.5 ± 9.7% over 5.7 years (log-rank P = 0.0001). Estimated median times to stage IV were 6.4, 5.3 and 3.8 years from stages I, II and III, respectively. Estimated median times to death were 10.9, 8.2, 6.3 and 1.7 years from stages I to IV, respectively. Results remained unchanged when CD4 lymphocyte count was replaced with lymphocyte count in the laboratory axis of the staging system. ConclusionsThe proposed staging scheme, based on the WHO system, provides a prognostically meaningful classification for HIV infection in a cohort of homosexual men. Furthermore, the use of absolute lymphocyte count as a valid alternative for CD4 lymphocyte count has implications for the applicability of this system in many parts of the world where diagnostic resources are limited.
Efficacy of Bifidobacterium breve and Lactobacillus casei oral supplementation on necrotizing enterocolitis in very-low-birth-weight preterm infants: a double-blind, randomized, controlled trial.

BACKGROUND Probiotics are used for the prevention of necrotizing enterocolitis (NEC) because of their positive effects on intestinal motor function, modulation of inflammatory response, and mucosal barrier function. OBJECTIVE The objective was to assess whether the combined use of Lactobacillus casei and Bifidobacterium breve may prevent the occurrence of NEC stage ≥ 2 by the criteria of Bell in very-low-birth-weight preterm infants. DESIGN A double-blind, randomized, controlled clinical trial was conducted in 231 preterm infants weighing from 750 to 1499 g at birth. The intervention group was composed of 119 infants who received human milk with probiotic supplementation (B. breve and L. casei) and a control group of 112 infants who received human milk containing no probiotics. The primary outcome was the occurrence of NEC stage ≥ 2 as defined by Bell's modified criteria. RESULTS Four confirmed cases of NEC stage ≥ 2 by Bell's criteria occurred only in the control group. CONCLUSIONS Oral supplementation of B. breve and L. casei reduced the occurrence of NEC (Bell's stage ≥ 2). It was considered that an improvement in intestinal motility might have contributed to this result. This trial was registered at www.isrctin. org as number 67165178 (International Standard Randomized Controlled Trial).
Proposed Use of Deoxycholic Acid ( DCA ) and Ursodeoxycholic Acid ( UDCA ) in a Treatment Regimen for Barrett ’ s Esophagus

Citation: Stamp D. (2016). Proposed Use of Deoxycholic Acid (DCA) and Ursodeoxycholic Acid (UDCA) in a Treatment Regimen for Barrett’s Esophagus. M J Canc. 1(2): 007. INTRODUCTION Huo et al [1] first placed 250 uM of the hydrophobic bile acid (DCA) into the esophagus of patients with Barrett’s esophagus (BE) and left it there for 5 min. The DCA was dissolved in alcohol. Subsequent examination of the biopsies taken from the esophagus showed that the DNA was damaged and the nuclear factor NF-kB was activated. Additionally, many other pre-cancerous lesions were activated. Similar treatment with the hydrophilic bile acid (UDCA) was ineffective, suggesting that UDCA could be an anti-carcinogen.
From Brain Imaging Religious Experience to Explaining Religion: A Critique

Recent functional neuroimaging data, acquired in studies of religious experience, have been used to explain and justify religion and its origins. In this paper, we critique the move from describing brain activity associated with self-reported religious states, to explaining why there is religion at all. Toward that end, first we review recent neuroimaging findings on religious experience, and show how those results do not necessarily support a popular notion that religion has a primitive evolutionary origin. Importantly, we call into question an assumption—key to that account of religion—concerning a conceptual relation between ‘religion’ and ‘religious experience’. Then, we examine the conditions that must be met in order to explain religion on the basis of brain imaging findings. Moreover, we list principled reasons to be sceptical of explanations of religion in terms of the neural underpinnings of experiences. We conclude that the data from neuroimaging studies are not suited for an explanation of religion.
Efficient Temporal Mean Shift for Activity Recognition in Video

We propose a temporal mean shift algorithm that clusters spatio-temporal regions in video by exploiting the temporal nature of video. Extracting spatio-temporal regions is often one of the first pre-processing steps in an activity recognition system. Our key contribution is the insight that mean shift clustering can exploit the fact that there is typically very little change between successive video frames. Most of the pixels, and therefore the clusters, shift only slightly from frame to frame. Since mean shift is an iterative procedure, fewer iterations are required for convergence if the initial search is already close to the local optimum. Our temporal mean shift algorithm exploits the temporal similarity between successive frames by initializing the search using the modes found in the previous frame. Standard Mean Shift Clustering •Finds local modes in the clusters of points •Iterative gradient ascent procedure •Let fi be a d-dimensional point in a set of n feature points f1.fn. We calculate where j = 1, 2, . , with kernel g, typically a Gaussian kernel, and bandwidth h. •The mode is the limit of the series, where y(i,j) converges to a fixed point. •The inner loop of mean shift requires a range-search of neighbors fk near y(i,j) , which is particularly time-consuming in high dimensions. •Previous methods in optimizing standard mean shift focused on reducing the time needed for range-search of neighbors. Temporal Mean Shift Clustering •We observe that in most videos, there is very little change between successive frames. Video sequence
Asymptotically distribution-free methods for the analysis of covariance structures.

Methods for obtaining tests of fit of structural models for covariance matrices and estimator standard errors which are asymptotically distribution free are derived. Modifications to standard normal theory tests and standard errors which make them applicable to the wider class of elliptical distributions are provided. A random sampling experiment to investigate some of the proposed methods is described.
BioC: a minimalist approach to interoperability for biomedical text processing

A vast amount of scientific information is encoded in natural language text, and the quantity of such text has become so great that it is no longer economically feasible to have a human as the first step in the search process. Natural language processing and text mining tools have become essential to facilitate the search for and extraction of information from text. This has led to vigorous research efforts to create useful tools and to create humanly labeled text corpora, which can be used to improve such tools. To encourage combining these efforts into larger, more powerful and more capable systems, a common interchange format to represent, store and exchange the data in a simple manner between different language processing systems and text mining tools is highly desirable. Here we propose a simple extensible mark-up language format to share text documents and annotations. The proposed annotation approach allows a large number of different annotations to be represented including sentences, tokens, parts of speech, named entities such as genes or diseases and relationships between named entities. In addition, we provide simple code to hold this data, read it from and write it back to extensible mark-up language files and perform some sample processing. We also describe completed as well as ongoing work to apply the approach in several directions. Code and data are available at http://bioc.sourceforge. net/. Database URL: http://bioc.sourceforge. net/
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$EVWUDFW The interaction with 3D scenes is an essential requirement of computer applications ranging from engineering and entertainment to architecture and social networks. Traditionally 3D scenes are rendered by projecting them onto a 2-dimensional surface such as a monitor or projector screen. This process results in the loss of several depth cues important for immersion into the scene. An improved 3D perception can be achieved by using immersive Virtual Reality equipment or modern 3D display devices. However, most of these devices are expensive and many 3D applications, such as modelling and animation tools, do not produce the output necessary for these devices. In this paper we explore the use of cheap consumer-level hardware to simulate 3D displays. We present technologies for adding stereoscopic 3D and motion parallax to 3D applications, without having to modify the source code. The developed algorithms work with any program that uses the OpenGL fixed-function pipeline. We have successfully applied the technique to the popular 3D modelling tool Blender. Our user tests show that stereoscopic 3D improves user's perception of depth in a virtual 3D environment more than head coupled perspective. However, the latter is perceived as more comfortable. A combination of both techniques achieves the best 3D perception, and has a similar comfort rating as stereoscopic 3D. In conventional applications, 3D scenes are rendered through a series of matrix transformations, which place objects in a virtual scene and project them towards a view plane. The resulting 2D images look flat and unrealistic because several depth cues are lost during the projection. Two important examples of cues are binocular parallax and motion parallax. These two depth cues are equally relevant when perceiving depth in a 3D environment (Rogers & Graham 1979). Hence it is desirable to recreate them to enhance the realism and presence in 3D scenes. Binocular parallax is the difference of images seen by each eye when viewing a scene, creating a sense of depth. In electronic media, this can be recreated using stereoscopic 3D (S3D) techniques, where different images are presented to each eye through a filtering mechanism. This is usually accomplished via 3D glasses worn by the user, e.g. when viewing 3D movies in the cinema. In computer applications there are several widely available implementations of stereoscopy, namely NVidia's 3D Vision Kit (NVidia 2011) and customised graphic drivers, such as iZ3D (iZ3D Software 2011) and TriDef (Dynamic Digital Depth 2011). Motion parallax …
Nasal airflow in inspiration and expiration

Abstract Inspiratory and expiratory airflow rates were measured in 30 subjects during quiet respiration (at a pressure gradient of 150 Pa) and at peak flow rates. For low flow rates airflow rate was greater for inspiration than for expiration. Conversely at peak flow rates flow was greatest during expiration. Thus there was a reversal in the phase relationship between inspiration and expiration as flow rate increased. It was also found that peak inspiratory flow rate correlated better with values for nasal resistance than did peak expiratory flow rate. Flow rate measured by rhinomanometry during quiet respiration was more sensitive to physiologically induced changes in nasal resistance than was peak flow rate. The findings are discussed with reference to previous work on the physiology of nasal airflow.
DAS28-CRP and DAS28-ESR cut-offs for high disease activity in rheumatoid arthritis are not interchangeable

Background In most patients with rheumatoid arthritis (RA), Disease Activity Score 28-joint count C reactive protein (DAS28-CRP) is lower than DAS28 erythrocyte sedimentation rate (DAS28-ESR), suggesting that use of the DAS28-ESR cut-off to assess high disease activity (HDA) with DAS28-CRP may underestimate the number of patients with HDA. We determined the DAS28-CRP value corresponding to the validated DAS28-ESR cut-off for HDA. Methods Baseline data were pooled from 2 clinical studies evaluating etanercept (ETN) plus methotrexate (MTX) or MTX in early RA; DAS28-CRP and DAS28-ESR were obtained, allowing the determination of the DAS28-CRP HDA value best corresponding to the DAS28-ESR cut-off of >5.1. Results At baseline, as expected, fewer patients had HDA by DAS28-CRP than DAS28-ESR; DAS28-CRP>5.1 and DAS28-ESR>5.1 had only modest agreement (κ coefficients 0.45–0.54). Mean DAS28-CRP and DAS28-ESR were 5.7 and 6.2, respectively, in the ETN+MTX group (n=571), and 6.0 and 6.5 in the MTX group (n=262). A DAS28-CRP cut-off of 4.6 corresponded to a DAS28-ESR cut-off of 5.1. Conclusions We have shown that a DAS28-CRP of 4.6 corresponds to 5.1 for DAS28-ESR. Since this is substantially lower than the DAS28-ESR cut-off of 5.1, using 5.1 as the cut-off for DAS28-CRP underestimates disease activity in RA. Trial registration number NCT00195494; NCT00913458.
Comparison of CHROMagar Salmonella Medium and Hektoen Enteric Agar for Isolation of Salmonellae from Stool Samples

ABSTRACT CHROMagar Salmonella (CAS), a new chromogenic medium, was retrospectively compared to Hektoen enteric agar (HEA) with 501Salmonella stock isolates and was then prospectively compared to HEA for the detection and presumptive identification ofSalmonella spp. with 508 stool samples before and after enrichment. All stock cultures (100%), including cultures of H2S-negative isolates, yielded typical mauve colonies on CAS, while 497 (99%) isolates produced typical lactose-negative, black-centered colonies on HEA. Following overnight incubation at 37°C, a total of 20 Salmonella strains were isolated from the 508 clinical samples. Sensitivities for primary plating and after enrichment were 95% (19 isolates) and 100% (20 isolates), respectively, for CAS and 80% (16 isolates) and 100% (20 isolates), respectively, for HEA. The specificity of CAS (88.9%) was significantly higher than that of HEA (78.5%; P < 0.0001). On the basis of its good sensitivity and specificity, CAS medium can be recommended for use for primary plating when human stool samples are screened for Salmonella spp.
Phenotypic Methods for Determining Genomovar Status of the Burkholderia cepacia Complex

ABSTRACT Recent taxonomic advances have demonstrated that Burkholderia cepacia is a cluster of at least seven closely related genomic species (or genomovars) collectively referred to as the B. cepacia complex, all of which may cause infections among cystic fibrosis patients and other vulnerable individuals. Thus, it is important for clinical microbiologists to be able to differentiate genomovars. Prior to this study, 361 B. cepacia complex isolates and 51 isolates easily confused with B. cepaciacomplex previously had been identified using a polyphasic approach, and in this study, a comparison of phenotypic and biochemical tests was carried out. It was determined that Burkholderia multivorans and Burkholderia stabilis could reliably be separated from other members of the B. cepacia complex by phenotypic methods. A combination of phenotypic and molecular tests such as recA PCR and 16S rRNA RFLP are recommended for differentiation among the genomovars of the B. cepaciacomplex. A biochemical reaction scheme for the identification ofB. gladioli, Pandoraea species, and Ralstonia pickettii and the differentiation of these species from theB. cepacia complex is also presented.
A low-cost embedded platform for car's surrounding vision system

The design and the implementation of a flexible and low-cost embedded system for car’s surrounding vision is presented. The target of the proposed multi-camera vision system is to provide the driver a better view of the objects that surround the vehicle during maneuvering. Fish-eye lenses are used to achieve a larger field of view (FOV) but, on the other hand, introduce radial distortion of the images projected on the sensors. Using low-cost cameras there could be also some alignment issues. Since these complications are noticeable and dangerous, a real-time algorithm for their correction and for the merging of 4 cameras video showed in a single view is presented.
Structural Control with Multi-Subnet Wireless Sensing Feedback: Experimental Validation of Time-Delayed Decentralized H* Control Design

This study investigates the feasibility of deploying wireless communication and embedded computing for structural control applications. A feedback structural control system involves a network of sensors and control devices. As control devices are becoming smaller, more cost effective and reliable, opportunities are now available to instrument a structure with large number of control devices. However, instrumenting a large scale centralized control system with cables can be time consuming, labor intensive, and difficult to maintain and reconfigure. This study explores decentralized feedback control using wireless sensors incorporated with a computational core and a signal generation module. Decentralized control architectures are designed to make control decisions based on data acquired from sensors located in the vicinity of a control device. Specifically, this paper describes the experimental validation of a time-delayed decentralized structural control strategy that aims to minimize the H* norm of a closed-loop control system. The decentralized controller design employs a homotopy method that gradually transforms a centralized controller into multiple decentralized controllers. Linear matrix inequality constraints are included in the homotopic transformation to ensure optimal control performance. The paper also describes our first implementation of a real-time wireless sensing and control system that achieves simultaneous communication within multiple wireless subnets. Different decentralized H* control architectures are implemented with a network of wireless sensing and control units instrumented on a six-story scaled steel frame structure controlled by magnetorheological dampers. Shake table experiments are conducted to demonstrate the performance of the wireless decentralized control architectures.
GeoSpark SQL: An Effective Framework Enabling Spatial Queries on Spark

In the era of big data, Internet-based geospatial information services such as various LBS apps are deployed everywhere, followed by an increasing number of queries against the massive spatial data. As a result, the traditional relational spatial database (e.g., PostgreSQL with PostGIS and Oracle Spatial) cannot adapt well to the needs of large-scale spatial query processing. Spark is an emerging outstanding distributed computing framework in the Hadoop ecosystem. This paper aims to address the increasingly large-scale spatial query-processing requirement in the era of big data, and proposes an effective framework GeoSpark SQL, which enables spatial queries on Spark. On the one hand, GeoSpark SQL provides a convenient SQL interface; on the other hand, GeoSpark SQL achieves both efficient storage management and high-performance parallel computing through integrating Hive and Spark. In this study, the following key issues are discussed and addressed: (1) storage management methods under the GeoSpark SQL framework, (2) the spatial operator implementation approach in the Spark environment, and (3) spatial query optimization methods under Spark. Experimental evaluation is also performed and the results show that GeoSpark SQL is able to achieve real-time query processing. It should be noted that Spark is not a panacea. It is observed that the traditional spatial database PostGIS/PostgreSQL performs better than GeoSpark SQL in some query scenarios, especially for the spatial queries with high selectivity, such as the point query and the window query. In general, GeoSpark SQL performs better when dealing with compute-intensive spatial queries such as the kNN query and the spatial join query.