gebhart/patrepeval huggingface dataset:
Candida dubliniensis: phylogeny and putative virulence factors (1998)

Candida dubliniensis is a recently identified species which is implicated in oral candidosis in HIV-infected and AIDS patients. The species shares many phenotypic characteristics with, and is phylogenetically closely related to, Candida albicans. In this study the phylogenetic relationship between these two species was investigated and a comparison of putative virulence factors was performed. Four isolates of C. dubliniensis from different clinical sources were chosen for comparison with two reference C. albicans strains. First, the distinct phylogenetic position of C. dubliniensis was further established by the comparison of the sequence of its small rRNA subunit with representative Candida species. The C. dubliniensis isolates formed true unconstricted hyphae under most induction conditions tested but failed to produce true hyphae when induced using N-acetylglucosamine. Oral C. dubliniensis isolates were more adherent to human buccal epithelial cells than the reference C. albicans isolates when grown in glucose and equally adherent when grown in galactose. The C. dubliniensis isolates were sensitive to fluconazole, itraconazole, ketoconazole and amphotericin B. Homologues of seven tested C. albicans secretory aspartyl proteinase (SAP) genes were detected in C. dubliniensis by Southern analysis. In vivo virulence assays using a systemic mouse model suggest that C. dubliniensis is marginally less virulent than C. albicans. These data further confirm the distinct phenotypic and genotypic nature of C. dubliniensis and suggest that this species may be particularly adapted to colonization of the oral cavity.
Very high efficiency VLSI chip-pair for full search block matching with fractional precision (2003)

VLSI architecture design and implementation of a chip pair for the motion compensation full search block matching algorithm are described. This pair of ASICs (application-specific integrated circuits) is motivated by the intensive computational demands for performing motion compensation in real time. They have been developed to calculate fractional motion vectors with quarter-pel precision. The VLSI architecture is based on some special data-flow designs that allow sequential inputs but perform parallel processing with 100% efficiency for integer motion vector estimation and nearly 100% for fractional motion vector estimation. The chip-pair design has been laid out and simulated using a silicon compiler tool, and the chip statistics are summarized. Testing circuitry is included to increase the observability of the chips.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Different Effects of BMP-2 on Marrow Stromal Cells from Human and Rat Bone (2004)

Bone morphogenetic proteins (BMPs) promote the differentiation of osteoprogenitor cells, and also induce osteogenesis in bone marrow stromal cells (MSC) from rats and mice. However, compared to results with animal models, BMPs are relatively inefficient in inducing human MSC to undergo osteogenesis, and are much less effective in promoting bone formation in human clinical trials. Previous studies indicated that, while human MSC respond to dexamethasone with elevated levels of the osteoblast marker alkaline phosphatase, most isolates of human MSC fail to show alkaline phosphatase induction in response to BMP-2, BMP-4, or BMP-7. Several other genes known to be induced by BMPs are appropriately regulated; thus, human MSC are capable of some BMP-activated signaling. Analysis of the BMP receptors ALK-3 and ALK-6 indicated that, although ALK-6 mRNA was not expressed in human MSC, overexpressing a constitutively active ALK-6 receptor did not induce elevated alkaline phosphatase. Real-time RT-PCR was used to investigate expression of several osteoblast-related transcription factors in MSC after 6 days' exposure to BMP2 or dexamethasone. Msx-2, a transcription factor that has been reported to inhibit differentiation of osteoprogenitor cells, showed 10-fold elevation in BMP-2-treated human MSC, but not in BMP-2-treated rat MSC. Overexpression of Msx-2 in human and rat MSC, however, did not alter alkaline phosphatase levels, which suggests that absence of BMP-stimulated alkaline phosphatase was not caused by the BMP-2-induced increase in Msx-2. Although Runx2 isoforms have been implicated in control of osteoblast differentiation, levels of this transcription factor were unaffected by BMP treatment. Expression of the FKHR transcription factor, which has been reported to regulate alkaline phosphatase transcription in mouse cells, showed a modest increase in response to BMP-2, but a much greater increase in dexamethasone-treated cells. We propose that BMP regulation of the bone/liver/kidney alkaline phosphatase gene is indirect, requiring expression of new transcription factor(s) that behave differently in rodent and human MSC.
Cu/Cu<sub>2</sub>O Electrodes and CO<sub>2</sub> Reduction to Formic Acid: Effects of Organic Additives on Surface Morphology and Activity (2016)

Copper/copper oxide (Cu/Cu<sub>2</sub> O) electrodes are known to display interesting electrocatalytic performances for the reduction of CO<sub>2</sub> , and thus, deserve further investigation for optimization. Here, we show that the addition of nitrogen-based organic additives greatly improves the activity of these electrodes (higher current densities, greater selectivity, and higher faradaic yields). The best effector is found to be tetramethyl cyclam. For example, electrolysis at -2.0 V versus Fc<sup>+</sup> /Fc in CO<sub>2</sub> -saturated DMF/H<sub>2</sub> O (99:1, v/v) in the presence of this effector results in formic acid with almost 90 % faradaic yield. SEM and XPS analysis of the electrode surface reveals that the organic additive promotes the formation of active Cu<sup>0</sup> nanoparticles from Cu<sub>2</sub> O during electrolysis. This simple approach provides a straightforward strategy toward the optimization of Cu/Cu<sub>2</sub> O electrodes.
Im/Mobility at the US–Mexico Border during the COVID-19 Pandemic (2021)

In March 2020, the United States government began a series of measures designed to dramatically restrict immigration as part of its response to the global health crisis caused by the coronavirus pandemic. This included Title 42, which deported asylum seekers immediately and prevented them from applying for asylum. These measures worsened an already precarious situation at the US–Mexico border for an estimated 60,000 asylum seekers who were prevented, by the Trump administration’s ‘Remain in Mexico’ (aka MPP) policy enacted in January 2019, from remaining in the United States while they awaited their asylum hearings. In-depth interviews, participant observation, and social media analysis with humanitarian and legal advocates for asylum seekers living in a camp at the border in Matamoros, Mexico reveal that COVID-19’s impacts are not limited to public health concerns. Rather, COVID-19’s impacts center on how the Trump administration weaponized the virus to indefinitely suspend the asylum system. We argue that the Matamoros refugee camp provides a strategic vantage point to understand the repercussions of state policies of exclusion on im/mobility and survival strategies for asylum seekers. Specifically, we use the analytical lenses of the politics of im/mobility, geographies of exclusion, and asylum seeker resilience to identify how COVID-19 has shaped the im/mobility and security of the camp and its residents in unexpected ways. At the same time, our research illustrates that camp residents exercise im/mobility as a form of political visibility to contest and ameliorate their precarity as they find themselves in conditions not of their choosing.
Measurement of Size and Distance of Objects Using Mobile Devices (2013)

This paper proposes methods for measuring size and distance of target objects by using mobile devices. For close-range measurement of a size of an object, users must hold the device close to the object and drag it along a desired direction. We develop a new approach for estimating a dragging distance of the device using acceleration signals retrieved from a three-axis accelerometer embedded on it. In the cases that target objects locate far from the device, users have to drag it vertically and two images of the objects are captured at starting and ending points of a dragging period. Then, the device displacement is estimated using acceleration signals, and a disparity of the object in two images is also determined via a matching technique based on Speeded Up Robust Features (SURF). The object disparity, dragging distance and device orientation are used as features to determine a distance between the target object and the device and also a size of it using learning-based scheme. Experimental results are presented to demonstrate a performance of the proposed methods.
A prospective, multicenter, randomized, controlled clinical trial comparing a bioengineered skin substitute to a human skin allograft. (2014)

An estimated 25% of all people with diabetes may experience a foot ulcer in their lifetime, which may lead to serious complications including infection and amputation. A prospective, multicenter, randomized, controlled clinical trial was conducted to compare an in vitro-engineered, human fibroblast-derived dermal skin (HFDS) substitute and a biologically active cryopreserved human skin allograft (HSA) to determine the relative number of diabetic foot ulcers (DFUs) healed (100% epithelialization without any drainage) and the number of grafts required by week 12. Secondary variables included the proportion of healed patients at weeks 16 and 20, time to healing during the study, and wound size progression. The 23 eligible participants (11 randomized to the HSA, 12 to the HFDS group) were recruited from two hospital-based outpatient wound care centers. Baseline patient (body mass index, age, gender, race, type and duration of diabetes, presence of neuropathy and/or peripheral arterial disease, tobacco use) and wound characteristics (size and duration) were recorded, and follow-up visits occurred every week for up to 20 weeks. Descriptive and multivariate regression analyses were used to compare wound outcomes. At baseline, no statistically significant differences between patients and wounds were observed. At week 12, seven (63.6%) patients in the HSA and four (33.3%) in the HFDS group were healed (P = 0.0498). At the end of the 20-week evaluation period, 90.91% of HSA versus 66.67% of HFDS were healed (P = 0.4282). Among the subset of wounds that healed during the first 12 weeks of treatment, an average of 4.36 (range 2-7) HSA grafts were applied versus 8.92 (range 6-12) in the HFDS subset (P <0.0001, SE 0.77584). Time to healing in the HSA group was significantly shorter (8.9 weeks) than in the HFDS group (12.5 weeks) (log-rank test, P = 0.0323). The results of this study are similar to previous outcomes reported using these treatment modalities and suggest that, after 12 weeks of care, DFUs managed with HSA are approximately twice as likely to heal as DFUs managed with HFDS with approximately half the number of grafts required. Research confirming these results with a larger sample size and inpatients with different types of wounds is warranted.
Fast Estimation of Large Displacement Optical Flow Using Dominant Motion Patterns & Sub-Volume PatchMatch Filtering (2017)

This paper presents a new method for efficiently computing large-displacement optical flow. The method uses dominant motion patterns to identify a sparse set of sub-volumes within the cost volume and restricts subsequent Edge-Aware Filtering (EAF) to these sub-volumes. The method uses an extension of PatchMatch to filter these sub-volumes. The fact that our method only applies EAF to a small fraction of the entire cost volume boosts runtime performance. We also show that computational complexity is linear in the size of the images and does not depend upon the size of the label space. We evaluate the proposed technique on MPI Sintel, Middlebury and KITTI benchmarks and show that our method achieves accuracy comparable to those of several recent state-of-the-art methods, while posting significantly faster runtimes.
Optical torques guiding cell motility (2009)

The main mechanism responsible for cell motility is the stochastic generation and breakup of actin filaments forming the cytoskeleton. However, the role of environmental factors in the migration and differentiation of cells is yet to be fully understood. Here we demonstrate that polarized optical fields can exert controllable torques on the actin network and therefore influence the treadmilling process responsible for cells motility. Through systematic experiments and stochastic modeling we demonstrate that actively guiding the dynamics of large groups of cells is possible in a noninvasive manner.
Towards transparent multi-device-authentication (2015)

Mobile devices are ubiquitous today and because they provide access to our digital lives, strong authentication is required to prevent unauthorized access. Commonly applied knowledge-based mechanisms like PIN and password, however, fail to scale with high frequency of device interactions and increasing number of mobile devices carried simultaneously. As a result, users are forced to authenticate dozens of times throughout the day and often disable authentication, choosing convenience over security. In our research, we aim to expand the concept of single-sign-on from a single device to all of the user's devices, allowing trusted devices within close proximity to securely and transparently share authentication information in order to gain sufficient confidence in the user's identity to omit explicit authentication.
A comprehensive formulation for volumetric modulated arc therapy planning (2016)

The novel nongreedy VMAT approach simultaneously optimizes all beams in an arc and then directly generates deliverable apertures. The single arc VMAT approach thus fully utilizes the digital Linac's capability in dose rate and gantry rotation speed modulation. In practice, the new single VMAT algorithm generates plans superior to existing VMAT algorithms utilizing two arcs.
Paramutation Alters Regulatory Control of the Maize pl Locus (2000)

The maize purple plant (pl) locus encodes a transcription factor required for anthocyanin pigment synthesis in vegetative and floral tissues. The strongly expressed Pl-Rhoades (Pl-Rh) allele is unstable, spontaneously changing to weaker expression states (Pl') at low frequencies and exclusively changing to Pl' in Pl'/Pl-Rh heterozygotes. The weakly expressed Pl' state is mitotically and meiotically stable, yet reversible. This type of allele-dependent, heritable alteration of gene control is called paramutation. Expression studies herein demonstrate that visible differences in anthocyanin pigment levels mirror pl RNA abundance and that pl paramutation is associated with reduced transcription of the pl gene. This transcriptional alteration is accompanied by acquisition of light-dependent regulation. Restriction endonuclease mapping indicates that these changes in pl gene regulation are not associated with detectable DNA alterations or with extensive changes in cytosine methylation patterns. Genetic tests show that Pl-Blotched (Pl-Bh), a structurally similar pl allele encoding an identical pl RNA and PL protein, does not participate in pl paramutation. This result suggests that if cis-acting sequences are required for pl paramutation they are distinct from the protein coding and immediately adjacent regions. A model is discussed in which pl paramutation results in heritable changes of chromatin structure that fundamentally alter regulatory interactions occurring during plant development.
Single-Dose Application of CNTF and BDNF Improves Remyelination of Regenerating Nerve Fibers after C7 Ventral Root Avulsion and Replantation (2008)

Although axonal regeneration has been observed after replantation of avulsed ventral roots (VR) into the spinal cord, the functional outcome of this treatment in terms of motor reinnervation is unsatisfactory. In the present study, effects of single-dose ciliary and/or brain-derived neurotrophic factor (CNTF, BDNF) application on axon regeneration after C7 VR avulsion and replantation in adult rabbits were morphologically assessed by analysis of numbers, calibers, and myelination of axons in replanted VRs. Electromyography (EMG) was carried out to document the time course of de- and reinnervation in individual animals. After 3 weeks, replanted C7 VRs were almost devoid of myelinated axons. At week 8, active EMG-denervation was confirmed in affected muscles, but was less pronounced in neurotrophic factor (NF)-treated animals than in controls. Reinnervation potentials were identified in paraspinal muscles in more NF-treated animals than in controls. After 6 months, the number of myelinated axons in replanted VRs was approximately 45% of that in unlesioned roots in all groups, with small-sized axons constituting the majority of axons. At this time, more NF-treated animals than controls featured reinnervation. Moreover, myelination deficits of regenerated axons in controls were less pronounced in NF-treated animals. Especially in CNTF + BDNF-treated animals, myelination of regenerated axons of specific sizes was significantly increased compared to regenerated controls. In summary, NFs stimulated reinnervation early after the lesion and, for the first time, our morphological data quantitatively indicate positive effects of CNTF + BDNF on remyelination.
Automatic detection and segmentation of renal lesions in 3D contrast-enhanced ultrasound images (2012)

Contrast-enhanced ultrasound (CEUS) is a valuable imaging modality in the detection and evaluation of different kinds of lesions. Three-dimensional CEUS acquisitions allow quantitative volumetric assessments and better visualization of lesions, but automatic and robust analysis of such images is very challenging because of their poor quality. In this paper, we propose a method to automatically segment lesions such as cysts in 3D CEUS data. First we use a pre-processing step, based on the guided filtering framework, to improve the visibility of the lesions. The lesion detection is then performed through a multi-scale radial symmetry transform. We compute the likelihood of a pixel to be the center of a dark rounded shape. The local maxima of this likelihood are considered as lesions centers. Finally, we recover the whole lesions volume with multiple front propagation based on image intensity, using a fast marching method. For each lesion, the final segmentation is chosen as the one which maximizes the gradient flux through its boundary. Our method has been tested on several clinical 3D CEUS images of the kidney and provides promising results.
Experimental Infection of Sheep with Bovine Leukemia Virus: Infectivity of Blood, Nasal and Saliva Secretions (1989)

This study was designed to determine the relative infectivity of lymphocytes and secretions from BLV-infected cattle with and without persistent lymphocytosis (BLV+PL+ and BLV+PL-). Ninety-seven sheep of mixed sex and age were assembled into 21 experimental groups. The recipient sheep were inoculated intravenously with serial dilutions of whole blood, saliva or nasal secretions from BLV+PL+ and BLV+PL- donor cows. Between 200 to 20,000 cells from single and mixed BLV+PL+ or single and mixed BLV+PL- donor cattle were used for inoculation. A very small number of BLV-infected lymphocytes (200 cells) was sufficient to induce BLV infection in sheep inoculated with diluted whole blood from BLV+PL+ cattle. The inoculation of whole blood (containing up to 20,000 lymphocyte cells) from BLV+PL- cattle did not induce BLV infection in recipient sheep. Saliva and nasal secretions also failed to bring about BLV transmission.
Combined static and dynamic automated test generation (2011)

In an object-oriented program, a unit test often consists of a sequence of method calls that create and mutate objects, then use them as arguments to a method under test. It is challenging to automatically generate sequences that are legal and behaviorally-diverse, that is, reaching as many different program states as possible.
Transverse Peltier effect in tilted Pb–Bi2Te3 multilayer structures (2006)

A transverse Peltier effect has been observed in artificially created tilted Pb–Bi2Te3 multilayer structures. Multilayer stacks consisting of alternating layers of Pb and n-type Bi2Te3 have been prepared by a heating procedure and showed large thermoelectric anisotropy up to ΔS≅200μV∕K, depending on thickness ratio p=dBiTe∕dPb, where dBiTe and dPb are the thicknesses of Bi2Te3 and Pb layers, respectively. Tilted samples were obtained by cutting stacks obliquely to the stack axis. Due to large ΔS and large electrical but small heat conductivity, samples showed temperature differences transverse to applied currents up to 22K.
Co-targeting of DNA, RNA, and protein molecules provides optimal outcomes for treating osteosarcoma and pulmonary metastasis in spontaneous and experimental metastasis mouse models (2017)

Metastasis is a major cause of mortality for cancer patients and remains as the greatest challenge in cancer therapy. Driven by multiple factors, metastasis may not be controlled by the inhibition of single target. This study was aimed at assessing the hypothesis that drugs could be rationally combined to co-target critical DNA, RNA and protein molecules to achieve "saturation attack" against metastasis. Independent actions of the model drugs DNA-intercalating doxorubicin, RNA-interfering miR-34a and protein-inhibiting sorafenib on DNA replication, RNA translation and protein kinase signaling in highly metastatic, human osteosarcoma 143B cells were demonstrated by the increase of γH2A.X foci formation, reduction of c-MET expression and inhibition of Erk1/2 phosphorylation, respectively, and optimal effects were found for triple-drug combination. Consequently, triple-drug treatment showed a strong synergism in suppressing 143B cell proliferation and the greatest effects in reducing cell invasion. Compared to single- and dual-drug treatment, triple-drug therapy suppressed pulmonary metastases and orthotopic osteosarcoma progression to significantly greater degrees in orthotopic osteosarcoma xenograft/spontaneous metastases mouse models, while none showed significant toxicity. In addition, triple-drug therapy improved the overall survival to the greatest extent in experimental metastases mouse models. These findings demonstrate co-targeting of DNA, RNA and protein molecules as a novel therapeutic strategy for the treatment of metastasis.
Intensity-modulated linear-frequency-modulated continuous-wave lidar for distributed media: fundamentals of technique (2010)

We analyze the intensity-modulation frequency-modulated continuous-wave (FMCW) technique for lidar remote sensing in the context of its application to distributed media. The goal of the technique is the reproduction of the sounded-medium profile along the emission path. A conceptual analysis is carried out to show the problems the basic version of the method presents for this application. The principal point is the appearance of a bandpass filtering effect, which seems to hinder its use in this context. A modified version of the technique is proposed to overcome this problem. A number of computer simulations confirm the ability of the modified FMCW technique to sound distributed media.
Early Use of PbS Nanotechnology for an Ancient Hair Dyeing Formula (2006)

Lead-based chemistry was initiated in ancient Egypt for cosmetic preparation more than 4000 years ago. Here, we study a hair-dyeing recipe using lead salts described in text since Greco-Roman times. We report direct evidence about the shape and distribution of PbS nanocrystals that form within the hair during blackening. It is remarkable that the composition and supramolecular organization of keratins can control PbS nanocrystal growth inside a hair.