gebhart/patrepeval huggingface dataset:
Bacterial Adrenergic Sensors Regulate Virulence of Enteric Pathogens in the Gut (2016)

The epinephrine and norepinephrine neurotransmitters play important roles in gut physiology and motility. Of note, epinephrine and norepinephrine play a central role in stress responses in mammals, and stress has profound effects on GI function. Bacterial enteric pathogens exploit these neurotransmitters as signals to coordinate the regulation of their virulence genes. The bacterial QseC and QseE adrenergic sensors are at the center of this regulatory cascade. C. rodentium is a noninvasive murine pathogen with a colonization mechanism similar to that of EHEC, enabling the investigation of host signals in mice. The presence of these neurotransmitters in the gut is necessary for C. rodentium to fully activate its virulence program, in a QseC/QseE-dependent manner, to successfully colonize its murine host. Our study data provide the first example of epinephrine and norepinephrine signaling within the gut to stimulate infection by a bacterial pathogen in a natural animal infection.
Surgical Management of Upper Tract Transitional Cell Carcinoma (2006)

Upper tract transitional cell carcinoma (TCC) accounts for approximately 5% of urothelial tumors. Surgical therapy for upper tract TCC is based on tumor grade, stage, location, and confounding factors of individual cases. Options for treatment range from minimally invasive procedures, such as ureteroscopy, to open nephroureterectomy. Laparoscopic nephroureterectomy is progressively eclipsing open nephroureterectomy in the surgical management of upper tract TCC. This article discusses the surgical options for managing upper tract TCC and their considerations for use.
Aptamer therapy for SCD? (2011)

In this issue of Blood , Gutsaeva et al describe an aptamer with high affinity for murine P-selectin and its efficacy in preventing vaso-occlusion in a mouse sickle cell disease (SCD) model.[1][1]

Each year, more than 200 000 children are born with SCD,[2][2] yet there is a paucity of treatment
Modeling of Acute Rectal Toxicity to Compare Two Patient Positioning Methods for Prostate Cancer Radiotherapy: Can Toxicity Modeling be Used for Quality Assurance? (2018)

Modeling of acute rectal toxicity provided a quantitative measure of the correlation between planning dosimetry and this clinical endpoint. Our study suggests that an unusually weak correlation may indicate a persistent patient positioning error.
Face recognition under variable pose and illumination conditions using 3D facial appearance models (2007)

Abstract This paper proposes a method in which an appearance model is constructed from 3D facial shape data that can describe the image variation due to the arbitrariness of the pose and the variation of the illumination, after which recognition is performed by fitting the model to facial images when the illumination conditions and the precise pose are unknown. The appearance model in the proposed method is constructed as follows. The illumination basis for an image of an arbitrary pose is derived from the geodesic illumination basis describing the brightness on the 3D object surface depending on the illumination variations, and an image with the same illumination condition is reproduced as the target image for the unknown illumination conditions. By optimizing the pose to minimize the reproduction error, model fitting with high accuracy is realized even if the exact pose is unknown. By experiment, the number of illumination samples needed in the calculation of the geodesic illumination basis is evaluated and it is verified that the proposed appearance model can describe arbitrary illumination variations in images with various poses. The robustness of the proposed pose optimization method against initial pose estimate is also evaluated. The effectiveness of the proposed method is demonstrated by a recognition experiment using 14,000 facial images taken in various situations, including extreme illumination variations such as backlighting, for a wide range of poses from frontal to 45 ° upward and 60 ° sidewise. © 2007 Wiley Periodicals, Inc. Syst Comp Jpn, 38(2): 57– 70, 2007; Published online in Wiley InterScience ( www.interscience. wiley.com ). DOI 10.1002/scj.20646
Sarcomas and Related Proliferative Lesions of Specialized Prostatic Stroma (1998)

Sarcomas and related proliferative lesions of the specialized prostatic stroma have been the subject of case reports and, thus, have not been well characterized. We reviewed the clinicopathologic features of 22 cases and studied the immunohistochemical profile of 9. Patient age ranged from 25 to 86 years; mean age was 54 years, and peak incidence was in the 6th and 7th decades. The most common clinical presentation was urinary retention, then abnormal results of digital rectal examination, hematuria or hematospermia, and a palpable rectal mass. The cases were grouped into two categories: prostatic stromal proliferation of uncertain malignant potential (PSPUMP, 18 cases) and prostatic stromal sarcoma (PSS, 4 cases) based on the degree of stromal cellularity and the presence of mitotic figures, necrosis, and stromal overgrowth. Four histologic patterns of PSPUMP were identified: (1) hypercellular stroma with scattered cytologically atypical cells associated with benign glands, (2) hypercellular stroma with minimal cytological atypia associated with benign glands, (3) hypercellular stroma with or without cytologically atypical cells, associated with benign glands in a "leaflike" growth pattern that resembled phyllodes tumors of the mammary gland, and (4) hypercellular stroma without cytologically atypical stromal cells and without glands. Prostatic stromal sarcoma showed greater cellularity, mitoses, necrosis, and stromal overgrowth than PSPUMP and consisted either of stromal elements with benign glands in a pattern that resembled malignant phyllodes tumors of the mammary gland (3 cases) or of purely stromal elements (1 case). Positive immunohistochemical reactions were noted using vimentin in 9 of 9 cases, CD34 in 8 of 8, HHF-35 in 2 of 8, smooth muscle actin in 3 of 9, desmin in 4 of 8, S-100 protein in 0 of 9, estrogen receptor in 1 of 7, and progesterone receptor in 6 of 7. None of the cases classified as PSS were positive for HHF-35, smooth muscle actin, or desmin. Of the 13 patients classified as having PSPUMP who did not undergo definitive local therapy at the time of diagnosis, recurrent signs or symptoms were seen in six (46%), necessitating additional therapy. Distant metastases to lung and bone developed in one patient classified as having PSS. Clinical and pathologic findings in this patient suggested a progression from PSPUMP to PSS. We conclude that sarcomas and related proliferative lesions of the specialized prostatic stroma encompass a spectrum of histologic features and may be grouped into two clinicopathologic categories: PSPUMP and PSS. Based on their distinctive histologic appearance and immunohistochemical profile, PSPUMP and PSS can be differentiated from other mesenchymal lesions of the prostate.
Synthesis and hydrophilicity of poly(butylene 2,6‐naphthalate)/poly(ethylene glycol) copolymers (2006)

Abstract Poly(butylene 2,6‐naphthalate) (PBN)/poly(ethylene glycol) (PEG) copolymers were synthesized by the two‐step melt copolymerization process of dimethyl‐2,6‐naphthalenedicarboxylate (2,6‐NDC) with 1,4‐butanediol (BD) and PEG. The copolymers produced had different PEG molecular weights and contents. The structures, thermal properties, and hydrophilicities of these copolymers were studied by 1 H NMR, DSC, TGA, and by contact angle and moisture content measurements. In particular, the intrinsic viscosities of PBN/PEG copolymers increased with increasing PEG molecular weights, but the melting temperatures ( T m ) , the cold crystallization temperatures ( T cc ) , and the heat of fusion (Δ H f ) values of PBN/PEG copolymers decreased on increasing PEG contents or molecular weights. The thermal stabilities of the copolymers were unaffected by PEG content or molecular weight. Hydrophilicities as determined by contact angle and moisture content measurements were found to be significantly increased on increasing PEG contents and molecular weights. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 100: 2677–2683, 2006
An analysis and validation pipeline for large-scale RNAi-based screens (2013)

Large-scale RNAi-based screens are a major technology, but require adequate prioritization and validation of candidate genes from the primary screen. In this work, we performed a large-scale pooled shRNA screen in mouse embryonic stem cells (ESCs) to discover genes associated with oxidative stress resistance and found several candidates. We then developed a bioinformatics pipeline to prioritize these candidates incorporating effect sizes, functional enrichment analysis, interaction networks and gene expression information. To validate candidates, we mixed normal cells with cells expressing the shRNA coupled to a fluorescent protein, which allows control cells to be used as an internal standard, and thus we could detect shRNAs with subtle effects. Although we did not identify genes associated with oxidative stress resistance, as a proof-of-concept of our pipeline we demonstrate a detrimental role of Edd1 silencing in ESC growth. Our methods may be useful for candidate gene prioritization of large-scale RNAi-based screens.
Characterization of the Stability of Indium Tin Oxide and Functional Layers for Semitransparent Back‐Contact Applications on Cu(in,Ga)Se2Solar Cells (2022)

Herein, a detailed study of the stability of different ITO‐based back‐contact configurations (including bare ITO contacts and contacts functionalized with nanometric Mo, MoSe 2 , and MoS 2 layers) under the coevaporation processes developed for the synthesis of high‐efficiency Cu(In,Ga)Se 2 (CIGSe) solar cells is reported. The results show that bare ITO layers can be used as efficient back contacts for coevaporation process temperatures of 480 ºC. However, higher temperatures produce an amorphous In–Se phase at the ITO surface that reduces the contacts transparency in the visible region. This is accompanied by degradation of the solar cells’ efficiency. Inclusion of a Mo functional layer leads to the formation of a MoSe 2 interfacial phase during the coevaporation process, which improves the cells’ efficiency, achieving device efficiencies similar to those obtained with reference solar cells fabricated with standard Mo back contacts. Optimization of the initial Mo layer thickness improves the contact transparency, achieving contacts with an optical transparency of 50% in the visible region. This is accompanied by a relevant decrease in back reflectivity in the CIGSe devices, confirming the potential of these contact configurations for the development of semitransparent CIGSe devices with improved optical aesthetic quality without compromising the device performance.
HM2-phage resistant solventogenic Clostridium saccharoperbutylacetonicum N1-4 shows increased exopolysaccharide production (2017)

During the history of the solventogenic clostridia fermentation industry, bacteriophages have been a recurrent problem. This study reports that HM2, a lytic bacteriophage for solventogenic Clostridium saccharoperbutylacetonicum N1-4 (N1-4), has a genome size of 17 470 bp with 22 open reading frames, including replication, lysis, integration and structural modules. To understand HM2 infection and resistance in N1-4, bacteriophage insensitive mutants (BIMs) were isolated and characterized. These eight independent BIMs included four adsorption mediated and four non-adsorption types. Adsorption mediated BIMs had increased exopolysaccharide (EPS) production and decreased attachment of HM2 to the cell surface. Non-adsorption mediated BIMs had a moderate increase in EPS production, which did not affect HM2 attachment. Absorption mediated BIMs had reduced fermentation performance, whereas the non-absorption mediated BIMs were indistinguishable from N1-4. Consequently, non-adsorption mediated BIMs would be more useful in a fermentation since they couple good fermentation performance with phage resistance.
Glucose-6-phosphate Dehydrogenase (G6PD) A-Variant Frequency and Novel Polymorphism in Haiti (2022)

There are scarce data about the glucose-6-phosphate dehydrogenase (G6PD) variants in Haiti to guide public health guidelines. In this study, we investigated the prevalence of the G6PD mutations related to the A- variant. We found an allelic frequency of 35.8% for the A376G mutation and of 12.2% for the G202A mutation. We also found a novel C370T mutation concomitant with the A376G mutation in one study participant. The G680T and T968C mutations were not found. The G6PD deficient variant A202 (A376G and G202A mutations) has appreciable prevalence in Haiti (16.6%), consideration is warranted when using drugs such as primaquine, which may trigger hemolytic anemia among G6PD-deficient people.
Synthesis, Optical and Structural Properties, and Charge Carrier Dynamics of Cu-Doped ZnSe Nanocrystals (2011)

Stable and luminescent Cu-doped ZnSe nanocrystals (NCs) were synthesized in organic solvents with octadecylamine (ODA) as the capping ligand and characterized using a combination of optical and structural characterization techniques. Successful doping was achieved by adding Cu during the growth phase of the NCs when their size was ∼4 nm. The appearance of red-shifted, intense photoluminescence (PL) peak with doping indicates the incorporation of Cu in the NCs, and stability of dopant emission infers the internal doping of NCs. Extended X-ray absorption fine structure (EXAFS) studies revealed that Cu is surrounded by four neighbors in the lattice but is very close to the NC surface and gets oxidized when NCs are precipitated from the solution. For the undoped sample, time-resolved PL studies using time-correlated single photon counting (TCSPC) reveal the luminescence decay lifetimes of about 1.1, 12, and 60 ns that we attribute to near-bandedge, shallow trap (ST) state, and deep trap (DT) state emissions, respectively. In addition to these decay components, the Cu-doped sample was found to have a long-lived component with a lifetime of 630 ns. Luminescence decay lifetimes of near-bandedge and ST state emissions were slightly shortened by doping (1 and 10 ns, respectively), suggesting that the Cu dopant competes with these states in trapping the charge carriers from the conduction band (CB) or near-bandedge states. However, the presence of Cu was found to increase the lifetime of DT states from 60 to 100 ns probably due to a decrease in coupling of electron and hole states involved in this emission upon Cu doping. Synthesis of such stable, doped samples along with a better understanding of charge carrier dynamics is significant for emerging optical applications of these NCs.
Regulation of 5′AMP-activated protein kinase activity and substrate utilization in exercising human skeletal muscle (2003)

The metabolic role of 5'AMP-activated protein kinase (AMPK) in regulation of skeletal muscle metabolism in humans is unresolved. We measured isoform-specific AMPK activity and beta-acetyl-CoA carboxylase (ACCbeta) Ser(221) phosphorylation and substrate balance in skeletal muscle of eight athletes at rest, during cycling exercise for 1 h at 70% peak oxygen consumption, and 1 h into recovery. The experiment was performed twice, once in a glycogen-loaded (glycogen concentration approximately 900 mmol/kg dry wt) and once in a glycogen-depleted (glycogen concentration approximately 160 mmol/kg dry wt) state. At rest, plasma long-chain fatty acids (FA) were twofold higher in the glycogen-depleted than in the loaded state, and muscle alpha1 AMPK (160%) and alpha2 AMPK (145%) activities and ACCbeta Ser(221) phosphorylation (137%) were also significantly higher in the glycogen-depleted state. During exercise, alpha2 AMPK activity, ACCbeta Ser(221) phosphorylation, plasma catecholamines, and leg glucose and net FA uptake were significantly higher in the glycogen-depleted than in the glycogen-loaded state without apparent differences in muscle high-energy phosphates. Thus exercise in the glycogen-depleted state elicits an enhanced uptake of circulating fuels that might be associated with elevated muscle AMPK activation. It is concluded that muscle AMPK activity and ACCbeta Ser(221) phosphorylation at rest and during exercise are sensitive to the fuel status of the muscle. During exercise, this dependence may in part be mediated by humoral factors.
Set It and Forget It: Approximating the Set Once Strip Cover Problem (2012)

We consider the Set Once Strip Cover problem, in which n wireless sensors are deployed over a one-dimensional region. Each sensor has a fixed battery that drains in inverse proportion to a radius that can be set just once, but activated at any time. The problem is to find an assignment of radii and activation times that maximizes the length of time during which the entire region is covered. We show that this problem is NP-hard. Second, we show that RoundRobin, the algorithm in which the sensors simply take turns covering the entire region, has a tight approximation guarantee of 3/2 in both Set Once Strip Cover and the more general Strip Cover problem, in which each radius may be set finitely-many times. Moreover, we show that the more general class of duty cycle algorithms, in which groups of sensors take turns covering the entire region, can do no better. Finally, we give an optimal O(n^2 log n)-time algorithm for the related Set Radius Strip Cover problem, in which all sensors must be activated immediately.
Chronic kidney disease and cognitive decline in patients with type 2 diabetes at elevated cardiovascular risk (2022)

NCT01897532 NCT01243424.
A compact LTCC Bluetooth system module with an integrated antenna (2006)

In this article, a system-on-package (SoP) approach for Bluetooth system module applications using low-temperature co-fired ceramic (LTCC) technology is presented. The developed LTCC integrated substrate for our Bluetooth module application is overall 12 × 12 × 1 mm3 in size, with integration of two originally proposed components, a balanced-to-unbalanced bandpass filter and a folded meander-line inverted-F antenna, as well as other passive circuitries. The embedded balanced-to-unbalanced filter, which is derived from the basic center-tapped transformer circuit, works simultaneously as a balun and a bandpass filter, thus leading to a significant amount of size reduction for the overall module. Likewise, comparing to the usual quarter-wavelength inverted-F antennas, our proposed antenna is only one-tenth of a wavelength in length—but no sacrificing of antenna efficiency. Consequently, couplings among different functional blocks of this highly integrated module are crucial to its performance and the resulting effects are discussed. A fully functional prototype is successfully fabricated and tested, demonstrating a promising solution for Bluetooth applications. © 2006 Wiley Periodicals, Inc. Int J RF and Microwave CAE, 2006.
Deformation profile of a piece of japonica cooked rice with squeezing test (2018)

The texture of cooked rice plays an important role in the characteristics of cooked rice. It can be firmness or stickiness depends on the amount of amylopectin inside the cooked rice, the higher the content will be more stickiness. Japonica rice is the type of rice with highest amylopectin content. Therefore the texture is the most stickiness. This research is to define the stickiness of japonica cooked rice using stress-strain behavior through uniaxial compression test. Stress defined as a normal force divided by a cross-sectional area in the horizontal plane while strain as a shrinking ratio of cooked rice. A single Japonica cooked rice squeezed using parallel plate type rheometer with constant velocity (0,2; 0,5; 1; 2; 4 mm/s). The deformation process of cooked rice was recorded from both side and bottom views to measure area transformation. The result showed that stress-strain of the deformation of cooked japonica rice was strongly depended on velocity. The low velocity (0,2;0,5;1 and 1 mm/s) are same with high velocity (2 and 4 mm/s) the during first deformation but significantly different statistically in the later deformation.
Negative-branch unstable resonator Nd:YAG laser (1976)

The results of an experimental investigation of the performance characteristics of a Q-switched Nd:YAG laser utilizing a negative-branch unstable resonator is presented. Measurements indicate that near diffraction-limited beam quality has been attained with a system in the rangefinder/designator energy category. In a performance comparison with a conventional parallel-plane mirror resonator, the unstable resonator was found to produce equally efficient operation with greatly superior beam radiance and tolerance to mirror misalignment.
A de novo variant in the X‐linked gene CNKSR2 is associated with seizures and mild intellectual disability in a female patient (2019)

Our results indicate that CNKSR2 nonsense variants in the C-terminal coding part can result in ID with seizures in female variant carriers.
Developmental Regulation of Microtubule‐Associated Protein 2 Expression in Regions of Mouse Brain (1989)

The relative levels of microtubule-associated protein 2(MAP2) were determined during postnatal development of the mouse in six different discrete brain regions: cerebellum, cortex, hippocampus, olfactory bulb, brainstem, and hypothalamus. Brain homogenates were electrophoresed on sodium dodecyl sulfate-containing gels and analyzed by immunoblotting with MAP2-specific antibodies. The levels of MAP2 in each region were determined using radiolabeled secondary antibodies and densitometric quantification of the autoradiograms over a range that was determined to have a linear response. The results indicated that in all regions and at all ages there was only one high-molecular-weight polypeptide of MAP2, which did not change in electrophoretic mobility after dephosphorylation. In most regions, the levels of MAP2 increased during the first 2 postnatal weeks. However, there were differences in the time course and relative levels of MAP2 between regions. In addition, all regions of the brain expressed the low-molecular-weight form of MAP2 (MAP2c) that was present at birth as a heterogeneous group of polypeptides with an apparent molecular weight of 70K. Most of the heterogeneity of MAP2c, however, was eliminated after dephosphorylation. The levels of MAP2c decreased dramatically after 2 weeks postnatally, except for the olfactory bulb, where the levels of MAP2c remained relatively high even in adults.
Using multi-layer distance maps for motion planning on surfaces with moving obstacles (2002)

This paper presents a new algorithm for planning the time-optimal motion of a robot traveling with limited velocity from a given location to a given destination on a surface in the presence of moving obstacles. Additional constraints such as space variant terrain traversability and fuel economy can be accommodated. A multilayer distance map is defined and applied in computing optimal trajectories. The multilayer distance map incorporates constraints imposed by the moving obstacles, surface topography and terrain traversability. It is generated by an efficient numerical curve propagation technique.
Isoproterenol inhibits rod outer segment phagocytosis by both cAMP-dependent and independent pathways. (1995)

Results suggest that FSK inhibits ROS phagocytosis by RPE cells through a cAMP-dependent pathway, whereas ISO inhibits ROS phagocytosis by RPE cells through cAMP-dependent and cAMP-independent pathways.