Miracle-dz/UniFAR-FTUs huggingface dataset:
A Real-Time PCR Assay for the Detection of Atypical Strains of Chlamydiaceae from Pigeons

Recent evidence of the occurrence of atypical Chlamydiaceae strains in pigeons, different from the established Chlamydiaceae, requires the development of a specific and rapid detection tool to investigate their prevalence and significance. Here is described a new real-time PCR assay that allows specific detection of atypical Chlamydiaceae from pigeons. The assay has been used to assess the dissemination of these strains in field samples collected from Parisian pigeon populations in 2009. The results suggest a limited dissemination compared to the usually higher prevalence of Chlamydia psittaci that is the main species associated with avian chlamydiosis.
Geometric Analysis of the Conformal Camera for Intermediate-Level Vision and Perisaccadic Perception

A binocular system developed by the author in terms of projective Fourier transform (PFT) of the conformal camera, which numerically integrates the head, eyes, and visual cortex, is used to process visual information during saccadic eye movements. Although we make three saccades per second at the eyeball's maximum speed of 700 deg/sec, our visual system accounts for these incisive eye movements to produce a stable percept of the world. This visual constancy is maintained by neuronal receptive field shifts in various retinotopically organized cortical areas prior to saccade onset, giving the brain access to visual information from the saccade's target before the eyes' arrival. It integrates visual information acquisition across saccades. Our modeling utilizes basic properties of PFT. First, PFT is computable by FFT in complex logarithmic coordinates that approximate the retinotopy. Second, a translation in retinotopic (logarithmic) coordinates, modeled by the shift property of the Fourier transform, remaps the presaccadic scene into a postsaccadic reference frame. It also accounts for the perisaccadic mislocalization observed by human subjects in laboratory experiments. Because our modeling involves cross-disciplinary areas of conformal geometry, abstract and computational harmonic analysis, computational vision, and visual neuroscience, we include the corresponding background material and elucidate how these different areas interwove in our modeling of primate perception. In particular, we present the physiological and behavioral facts underlying the neural processes related to our modeling. We also emphasize the conformal camera's geometry and discuss how it is uniquely useful in the intermediate-level vision computational aspects of natural scene understanding.
Pediatric Intracranial Aneurysms : Endovascular Treatment

© 2015 Egyptian Journal of Neurosurgery. All rights reserved Background: Intracranial aneurysms are rare in pediatric age group. Their clinicoradiological features may differ from those in adults. Objective: The aim of this study was to analyze clinical presentation, location and morphological characteristics of pediatric age aneurysm with assessment of feasibility, safety and efficacy of endovascular treatment. Patients and Methods: A retrospective study was conducted on patients with intracranial aneurysm aged 18 years or younger who underwent endovascular treatment in the period between July 2006 and July 2014 in the Departments of Neurosurgery in Ain Shams University and Souhag University. Data were collected and analyzed as regard: presenting symptom, aneurysm characteristics (site, size and subtype), endovascular management, and procedure clinic-radiological outcome and follow up were analyzed. There were twenty-two patients with twenty-two aneurysms, age range 1.5 to 17 years with a mean of 10.97±4.69, 13 males and 9 females. Results: Subarachnoid hemorrhage was the main presentation with a rate of 54.4%, and the rate of associated underlying diseases was 40.9%. Saccular aneurysms (without clinical association of infection or trauma) were found in ten patients (45.5%), dissecting fusiform (without clinical association of infection or trauma) in seven patients (31.8%), infectious in three patients (13.6%) and traumatic in two patients (9.1%). Five aneurysms (22.7%) were located in the posterior circulation, while six were located at internal carotid artery (ICA) termination (27.3%). Five aneurysms (22.7%) were giant aneurysms. Endovascular coiling was done in thirteen aneurysms (59.1%): ten were saccular, two traumatic, and one dissecting fusiform. Parent vessel occlusion was done in nine aneurysms (40.1%), three were infectious (glue was used), and six were fusiform aneurysms (four by detachable balloons and two by coils). Immediate angiographic cure was seen in twenty aneurysms (90.9%) and remaining two aneurysms had small neck residual. Recanalization at one year follow up occurred in three aneurysms (13.6%), two of which needed further endovascular treatment. There was no rebleeds during the follow up period. The rate of permanent procedure related complication and favorable outcome were 4.55% and 90.9% respectively. Conclusion: Pediatric intracranial aneurysms are a rare entity with different characteristics than adult aneurysms. In pediatric aneurysms association of an underlying disease should be considered. The rate of giant, dissecting fusiform and mycotic aneurysms is more common then in adults. ICA bifurcation and posterior circulation located aneurysms have higher incidence in pediatric patients than adults do. Endovascular treatment with different techniques is considered technically feasible, relatively safe and efficient with high favorable outcome and low rates of mortality and morbidity, yet longer period of follow up is needed to assure long term safety.
Breakdown of universality in multi-cut matrix models

We solve the puzzle of the disagreement between orthogonal polynomials methods and mean-field calculations for random N×N matrices with a disconnected eigenvalue support. We show that the difference does not stem from a 2 symmetry breaking, but from the discreteness of the number of eigenvalues. This leads to additional terms (quasiperiodic in N) which must be added to the naive mean-field expressions. Our result invalidates the existence of a smooth topological large-N expansion and some postulated universality properties of correlators. We derive the large-N expansion of the free energy for the general two-cut case. From it we rederive by a direct and easy mean-field-like method the two-point correlators and the asymptotic orthogonal polynomials. We extend our results to any number of cuts and to non-real potentials.
Integration of spatio-temporal contrast sensitivity with a multi-slice channelized Hotelling observer

Barten’s model of spatio-temporal contrast sensitivity function of human visual system is embedded in a multi-slice channelized Hotelling observer. This is done by 3D filtering of the stack of images with the spatio-temporal contrast sensitivity function and feeding the result (i.e., the perceived image stack) to the multi-slice channelized Hotelling observer. The proposed procedure of considering spatio-temporal contrast sensitivity function is generic in the sense that it can be used with observers other than multi-slice channelized Hotelling observer. Detection performance of the new observer in digital breast tomosynthesis is measured in a variety of browsing speeds, at two spatial sampling rates, using computer simulations. Our results show a peak in detection performance in mid browsing speeds. We compare our results to those of a human observer study reported earlier (I. Diaz et al. SPIE MI 2011). The effects of display luminance, contrast and spatial sampling rate, with and without considering foveal vision, are also studied. Reported simulations are conducted with real digital breast tomosynthesis image stacks, as well as stacks from an anthropomorphic software breast phantom (P. Bakic et al. Med Phys. 2011). Lesion cases are simulated by inserting single micro-calcifications or masses. Limitations of our methods and ways to improve them are discussed.
The relationship of lower-extremity muscle torque to locomotor performance in people with stroke.

BACKGROUND AND PURPOSE Improved walking is a common goal after stroke. The purpose of this study was to examine the relationship between the torque generated by the muscles of both lower extremities and 2 locomotor tasks: gait on level surfaces and stair climbing in people who had strokes. SUBJECTS Twenty community-dwelling individuals (mean age=61.2 years, SD=8.4, range=52-82) who had strokes and who were able to walk independently participated in the study. The mean time since stroke was 4.0 years (SD=2.6, range=1.5-10.0). METHODS Pearson correlations and multiple regression were used to measure the relationship between concentric isokinetic torque of the flexor and extensor muscles of the hip, knee, and ankle bilaterally and locomotor performance (gait on level surfaces and stair-climbing speed). RESULTS The isokinetic torques of the paretic ankle plantar flexors, hip flexors, and knee flexors had moderate to high correlations (r=.5-.8) with gait and stair-climbing speeds. Muscle force could explain 66% to 72% of the variability in gait and stair-climbing speeds. Correlations for the nonparetic side were as high as or higher than those for the paretic side for some muscle groups. DISCUSSION AND CONCLUSION Muscle performance measurements of both limbs should be included in the evaluation of locomotion and treatment of people following a stroke.
Inhibition of Wnt signaling by the osteoblast-specific transcription factor Osterix

The recent identification of the genes responsible for several human genetic diseases affecting bone homeostasis and the characterization of mouse models for these diseases indicated that canonical Wnt signaling plays a critical role in the control of bone mass. Here, we report that the osteoblast-specific transcription factor Osterix (Osx), which is required for osteoblast differentiation, inhibits Wnt pathway activity. First, in calvarial cells of embryonic day (E)18.5 Osx-null embryos, expression of the Wnt antagonist Dkk1 was abolished, and that of Wnt target genes c-Myc and cyclin D1 was increased. Moreover, our studies demonstrated that Osx bound to and activated the Dkk1 promoter. In addition, Osx inhibited β-catenin-induced Topflash reporter activity and β-catenin-induced secondary axis formation in Xenopus embryos. Importantly, in calvaria of E18.5 Osx-null embryos harboring the TOPGAL reporter transgene, β-galactosidase activity was increased, suggesting that Osx inhibited the Wnt pathway in osteoblasts in vivo. Our data further showed that Osx disrupted binding of Tcf to DNA, providing a likely mechanism for the inhibition by Osx of β-catenin transcriptional activity. We also showed that Osx decreased osteoblast proliferation. Indeed, E18.5 Osx-null calvaria showed greater BrdU incorporation than wild-type calvaria and that Osx overexpression in C2C12 mesenchymal cells inhibited cell growth. Because Wnt signaling has a major role in stimulating osteoblast proliferation, we speculate that Osx-mediated inhibition of osteoblast proliferation is a consequence of the Osx-mediated control of Wnt/β-catenin activity. Our results add a layer of control to Wnt/β-catenin signaling in bone.
On the long-range dependence of packet round-trip delays in Internet

Many previous studies on network traffic demonstrate that long-range dependence (LRD) is a ubiquitous property of traffic both in a local area network (LAN) and a wide area network (WAN). So the performance of the network should be dominated by this property. The packet round-trip delay is an important measurement of network performance. We present evidence that LRD exists in packet round-trip delays. This discovery has serious implications for understanding the impact on network performance of LRD network traffic, and the design of transport control protocols for special applications, i.e., of teleconferencing. Statistical analyses show that the complementary probability distribution of packet round-trip delays decays more slowly than at an exponential rate; this fact probably justifies the studies on the prediction of the queue length distribution with LRD network traffic. We also tentatively use a multi-queueing system to interpret the existence of LRD in the packet round-trip delay process, which we believe is caused by the LRD of Internet traffic.
Bracketing Metric Entropy Rates for Function Classes of Besov-and Sobolev-Type De ned on Borel Sets of R d

We derive L ( )-bracketing metric and sup-norm metric entropy rates of various subsets of general function spaces de ned over R or, more generally, over Borel sets , exploiting results by Haroske and Triebel (1994, 2004). The function spaces covered are of (fractional) Sobolev, Besov, Hölder, Triebel, and Bessel Potential type. Applications to the theory of empirical processes are discussed. In particular, we show that (weighted) norm balls in the above mentioned spaces are Donsker classes uniformly in various sets P of probability measures. MSC 2000 subject classi cation. Primary 60F17; secondary 46E35
Culture and Use of Mesenchymal Stromal Cells in Phase I and II Clinical Trials

Present in numerous tissues, mesenchymal stem cells/multipotent stromal cells (MSCs) can differentiate into different cell types from a mesoderm origin. Their potential has been extended to pluripotency, by their possibility of differentiating into tissues and cells of nonmesodermic origin. Through the release of cytokines, growth factors and biologically active molecules, MSCs exert important paracrine effects during tissue repair and inflammation. Moreover, MSCs have immunosuppressive properties related to non-HLA restricted immunosuppressive capacities. All these features lead to an increasing range of possible applications of MSCs, from treating immunological diseases to tissue and organ repair, that should be tested in phase I and II clinical trials. The most widely used MSCs are cultured from bone marrow or adipose tissue. For clinical trial implementation, BM MSCs and ADSCs should be produced according to Good Manufacturing Practices. Safety remains the major concern and must be ensured during culture and validated with relevant controls. We describe some applications of MSCs in clinical trials.
Endoscopic Findings of Gastric Extranodal Marginal Zone B-Cell Mucosa-Associated Lymphoid Tissue Lymphoma

Approximately 360,000 new cases of non-Hodgkin’s lymphoma were diagnosed worldwide in 2014. Of these, approximately 7% were diagnosed with mucosa-associated lymphoid tissue (MALT) lymphoma. Gastric extranodal marginal zone B-cell MALT lymphoma accounts for 1%–7% of malignant gastric tumors and 60%–75% of gastrointestinal MALT lymphomas. Gastric MALT lymphoma shows various endoscopic findings. The structure and function of gastric MALT are similar to those of Peyer’s patches in the terminal ileum. Gastric MALT originates in subepithelial layers, usually in the stromal space, and grows under the normal gastric foveolar glands. Thus, both mucosal and submucosal lesions can be found on endoscopic examination. Therefore, the histologic diagnosis of lymphoma is often unexpected, even to an experienced endoscopist. Taal et al. attempted to classify the endoscopic findings in gastric MALT lymphoma into several categories. Thereafter, several classification systems based on gross morphology were suggested. However, there have been no generally accepted classification criteria, because the clinical implications of endoscopic categorization of gastric MALT lymphoma are still unclear. Advanced stage, gene translocation t(11;18) (q21;q21), and non-responder (no change) MALT lymphomas that persist after successful Helicobacter pylori eradication are associated with poor prognosis. In addition to those factors, Lee et al. in this issue of Clinical Endoscopy, concluded that the endoscopically defined polypoid type is associated with poor prognosis, and is characterized by a longer duration to complete response (CR), with a higher likelihood of recurrence, compared to the endoscopically defined diffuse infiltration or ulceration types. However, caution is needed when interpreting the results of this study. Even though the authors stated that there was no significant colinearity between endoscopic findings, Ann Arbor stage, and/or treatment, one of the three variables could be a potential confounding factor, as the authors suggested. With reference to their data summarized in the table, polypoid lesions are more likely to be diagnosed at an advanced Ann Arbor stage, as compared to diffuse infiltration or ulceration types. In a review of previous reports, Yokoi et al. suggested that the pathogenesis of polypoid gastric MALT lymphoma has little association with H. pylori infection. However, the results of this study are different from those in Yokoi’s report. Thus, it is still uncertain whether there is a reasonable explanation for a causal relationship between polypoid gastric MALT lymphoma and poor prognosis. We hope that a follow-up study can demonstrate a correlation between polypoid MALT lymReceived: December 15, 2016 Revised: January 18, 2017 Accepted: January 18, 2017 Correspondence: Sang Kill Lee Division of Gastroenterology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea Tel: +82-2-2228-2272, Fax: +82-51-244-8180, E-mail: SKLEE@yuhs.ac
Neurons in the Primate Medial Basal Forebrain Signal Combined Information about Reward Uncertainty, Value, and Punishment Anticipation

It has been suggested that the basal forebrain (BF) exerts strong influences on the formation of memory and behavior. However, what information is used for the memory-behavior formation is unclear. We found that a population of neurons in the medial BF (medial septum and diagonal band of Broca) of macaque monkeys encodes a unique combination of information: reward uncertainty, expected reward value, anticipation of punishment, and unexpected reward and punishment. The results were obtained while the monkeys were expecting (often with uncertainty) a rewarding or punishing outcome during a Pavlovian procedure, or unexpectedly received an outcome outside the procedure. In vivo anterograde tracing using manganese-enhanced MRI suggested that the major recipient of these signals is the intermediate hippocampal formation. Based on these findings, we hypothesize that the medial BF identifies various contexts and outcomes that are critical for memory processing in the hippocampal formation.
Analytic modeling of interconnect capacitance in submicron and nanometer technologies

Parasitic capacitance of interconnects in the analog and mixed-signal VLSI circuits can be modeled by using physics equations or empirical curve fitting. In this paper, we propose an analytical model for computing parasitic capacitance between interconnects on different layers or on the same layer. In our method, electric flux is approximated to model different capacitive components, which combine to determine the overall equivalent capacitance. We first derive a general template for the fringe capacitance based on fundamental electromagnetic principles, followed by a fitting technique in order to reach outstanding accuracy. Based on our approach that includes no complex operators, capacitance of typical interconnect geometries can be efficiently computed. The proposed model is verified in comparison with the extracted results derived from commercial tools. The experimental results show that our proposed method can best approach the extracted results yet with significantly reduced computation time.
Anti-CD70 antibodies: a potential treatment for EBV+ CD70-expressing lymphomas

A monoclonal antibody (Rituximab) directed against the B-cell surface antigen, CD20, is increasingly used as a therapy for B-cell lymphomas. However, CD20 is expressed on all normal mature B cells and hence is not a specific tumor target. In contrast, CD70 is expressed on highly activated lymphocytes as well as on many B-cell and T-cell lymphomas but is not expressed on the great majority of B cells and T cells. In this report, we have explored the potential utility of anti-CD70 monoclonal antibodies for treatment of CD70+ EBV+ B-cell lymphomas. Using two Burkitt's lymphoma lines (Raji and Jijoye) that express surface CD70 and a CD70− Burkitt's lymphoma line (Akata), we show that two different monoclonal antibodies directed against human CD70 allow rabbit and human complement to kill EBV+ B cells in a CD70-dependent manner in vitro. In the absence of complement, neither anti-CD70 antibody induced in vitro killing of CD70+ cell lines. Importantly, i.p. injection of anti-CD70 antibodies also inhibited the growth of CD70+ Burkitt's lymphoma cells in severe combined immunodeficient mice but did not inhibit the growth of CD70− Burkitt's lymphoma cells. These results suggest that anti-CD70 antibodies may be useful for the treatment of CD70+ B-cell lymphomas. [Mol Cancer Ther 2005;4(12):2037–44]
In Vitro Evaluation of Horizontal Implant Micromovement in Bone Specimen With Contact Endoscopy

Primary stability of dental implants is mandatory for their osseointegration. A method is described that allows objective measurements of implant displacement in bone sites during lateral loading. Ten samples of bovine bone (2 cm × 2 cm) with bone type II, III, and IV according to Lekholm and Zarb were used for the experiment. Ten Semados dental implants of 15-mm length and 3.75-mm diameter were placed. All implants were loaded with lateral forces of 5, 10, 20, and 30 N through 8-mm abutments for 2 seconds each. Lateral displacement was observed by means of contact endoscopy. Micromovement was detected with the help of a transmitter strip attached to the abutment. Endoscopic images were processed digitally and microdis- placement was calculated relative to the reference body (microscrew) placed adjacent to the implant. Micromovement observed varied with the force applied. Lateral force of 5 N resulted in a mean displacement of 39 &mgr;m; for 30 N, the mean displacement was 157 &mgr;m. Bone type also influenced the amount of movement. Contact endoscopy represents a new method for direct observation of implant movement relative to the bone surface in vitro. In combination with support immersion technique, contact endoscopy could be used as an office procedure to evaluate intraoperatively implant stability during functional loading.
Role of metabolic stress for enhancing muscle adaptations: Practical applications

Metabolic stress is a physiological process that occurs during exercise in response to low energy that leads to metabolite accumulation [lactate, phosphate inorganic (Pi) and ions of hydrogen (H+)] in muscle cells. Traditional exercise protocol (i.e., Resistance training) has an important impact on the increase of metabolite accumulation, which influences hormonal release, hypoxia, reactive oxygen species (ROS) production and cell swelling. Changes in acute exercise routines, such as intensity, volume and rest between sets, are determinants for the magnitude of metabolic stress, furthermore, different types of training, such as low-intensity resistance training plus blood flow restriction and high intensity interval training, could be used to maximize metabolic stress during exercise. Thus, the objective of this review is to describe practical applications that induce metabolic stress and the potential effects of metabolic stress to increase systemic hormonal release, hypoxia, ROS production, cell swelling and muscle adaptations.