gebhart/patrepeval huggingface dataset:
Comparative genetic analysis of trichome-less and normal pod genotypes of Mucuna pruriens (Fabaceae) (2011)

Velvet bean (Mucuna pruriens) seeds contain the catecholic amino acid L-DoPA (L-3,4-dihydroxyphenylalanine), which is a neurotransmitter precursor and used for the treatment of Parkinson's disease and mental disorders. The great demand for L-DoPA is largely met by the pharmaceutical industry through extraction of the compound from wild populations of this plant; commercial exploitation of this compound is hampered because of its limited availability. The trichomes present on the pods can cause severe itching, blisters and dermatitis, discouraging cultivation. We screened genetic stocks of velvet bean for the trichome-less trait, along with high seed yield and L-DoPA content. The highest yielding trichome-less elite strain was selected and indentified on the basis of a PCR-based DNA fingerprinting method (RAPD), using deca-nucleotide primers. A genetic similarity index matrix was obtained through multivariant analysis using Nei and Li's coefficient. The similarity coefficients were used to generate a tree for cluster analysis using the UPGMA method. Analysis of amplification spectra of 408 bands obtained with 56 primers allowed us to distinguish a trichome-less elite strain of M. pruriens.
Directed assembly in epitaxial zinc oxide films on focused ion beam modified sapphire substrates (2011)

A new method for directed self-assembly using focused ion beam (FIB) and physical vapor deposition is presented. The high resolution and site-specific patterning capabilities of FIB are coupled with the self-assembly process in heteroepitaxial thin film growth. An efficient FIB-induced damage mechanism is exploited to pattern amorphous regions in sapphire substrates which direct the subsequent assembly of a sputter-deposited zinc oxide film. This novel approach allows for the fabrication of in-plane nano- to microscale heterostructures comprising epitaxial regions with high strain and defect density that are separated by regions of randomly oriented (in-plane) grains with much lower strain and defect density.
A Sensitive Resonant Gas Sensor Based on Multimode Excitation of a Buckled Beam (2019)

Abstract The quest for ultra-sensitive low-cost miniaturized gas sensors in the past few decades has sparked interest to seek alternative approaches other than the conventional gas sensors that need large surface areas and special chemicals for functionalization. MEMS thermal conductivity based gas sensors [1, 2] have been shown to be among the promising candidates since they do not rely on gas absorption or chemical reactions. These sensors show long lifetime and great stability compared to conventional gas sensor. The thermal conductivity based gas sensors rely on the resistance variation of the heated structures due to gas exposure [1]. Typical values of resistance changes are less than few percent. Here, we present a thermal conductivity based gas sensor relying on frequency shifts of an electrothermally heated bridge operated near the buckling point, which leads to ultra-high sensitivity.
Fibre tract analysis using diffusion tensor imaging reveals aberrant connectivity in a rat model of depression (2016)

Decreased connectivity in a genetic rat model of depression corroborates the findings in patients suffering from major depression suggesting that the vulnerability for developing depression is mainly polygenic and less likely to be due to childhood adversity per se.
Nanometers-Thick Ferromagnetic Surface Produced by Laser Cutting of Diamond (2022)

In this work, we demonstrate that cutting diamond crystals with a laser (532 nm wavelength, 0.5 mJ energy, 200 ns pulse duration at 15 kHz) produced a ≲20 nm thick surface layer with magnetic order at room temperature. We measured the magnetic moment of five natural and six CVD diamond crystals of different sizes, nitrogen contents and surface orientations with a SQUID magnetometer. A robust ferromagnetic response at 300 K was observed only for crystals that were cut with the laser along the (100) surface orientation. The magnetic signals were much weaker for the (110) and negligible for the (111) orientations. We attribute the magnetic order to the disordered graphite layer produced by the laser at the diamond surface. The ferromagnetic signal vanished after chemical etching or after moderate temperature annealing. The obtained results indicate that laser treatment of diamond may pave the way to create ferromagnetic spots at its surface.
Metal Complexes with Azolate‐Functionalized Multidentate Ligands: Tactical Designs and Optoelectronic Applications (2016)

This review is aimed at updating the recent development on the metal complexes bearing azolate-containing chelates that have received a growing attention from both the industrial and academic sectors. Particular emphasis is given to the luminescent metal complexes, for which tridentate and multidentate bonding interactions give rise to both higher ligand field strength and better rigidity versus their bidentate counterparts-consequently, this is beneficial to the chemical stability and emission efficiency needed for applications such as organic light-emitting diodes and bio-imaging. Their basic designs involve chelates, such as monoanionic 6-azolyl 2,2'-bipyridine, dianionic 2,6-diazolylpyridine, and 2-azolyl-6-phenylpyridine, and the core metal ion spanning from main group elements, such as Ga<sup>III</sup> and In<sup>III</sup> , to the late transition metal ions such as Ru<sup>II</sup> , Os<sup>II</sup> , Ir<sup>III</sup> , and Pt<sup>II</sup> and even the lanthanides. Furthermore, the great versatility of these azolate chelates for assembling the robust and emissive metal complexes, provides bright prospect in future optoelectronic investigations.
Dijet Azimuthal Decorrelations inppCollisions ats=7  TeV (2011)

Measurements of dijet azimuthal decorrelations in pp collisions at √s=7 TeV using the CMS detector at the CERN LHC are presented. The analysis is based on an inclusive dijet event sample corresponding to an integrated luminosity of 2.9 pb⁻¹. The results are compared to predictions from perturbative QCD calculations and various Monte Carlo event generators. The dijet azimuthal distributions are found to be sensitive to initial-state gluon radiation.
The First Potent Inhibitor of Mammalian Group X Secreted Phospholipase A2:  Elucidation of Sites for Enhanced Binding (2006)

Using the X-ray structure of human group X secreted phospholipase A(2) (hGX), we carried out structure-based design of indole-based inhibitors and prepared the compounds using a new synthetic route. The most potent compound inhibited hGX and the mouse orthologue with an IC(50) of 75 nM. This compound is the most potent hGX inhibitor reported to date and was also found to inhibit a subset of the other mouse and human sPLA(2)s.
Structural Optimization of Quinolon-4(1H)-imines as Dual-Stage Antimalarials: Toward Increased Potency and Metabolic Stability (2013)

Discovery of novel effective and safe antimalarials has been traditionally focused on targeting erythrocytic parasite stages that cause clinical symptoms. However, elimination of malaria parasites from the human population will be facilitated by intervention at different life-cycle stages of the parasite, including the obligatory developmental phase in the liver, which precedes the erythrocytic stage. We have previously reported that N-Mannich-based quinolon-4(1H)-imines are potent antiplasmodial agents but present several stability liabilities. We now report our efforts to optimize quinolon-4(1H)-imines as dual-stage antiplasmodial agents endowed with chemical and metabolic stability. We report compounds active against both the erythrocytic and exoerythrocytic forms of malaria parasites, such as the quinolon-4(1H)-imine 5p (IC50 values of 54 and 710 nM against the erythrocytic and exoerythrocytic forms), which constitute excellent starting points for further lead optimization as dual-stage antimalarials.
Kidney segmentation from a single prior shape in MRI (2014)

This paper reports a novel approach to 3D kidney segmentation from a single prior shape in magnetic resonance imaging (MRI) datasets. The proposed method is based on a hierarchic surface deformation algorithm, to generate a pre-personalized model, followed by an anamorphing segmentation algorithm, to extract the kidney capsule. Accuracy and precision are assessed by comparing our method over 20 kidney reconstructions segmented manually by 3 different observers on native MRI images. The experimental results show a volumetric overlap error of 6.39±2.47%, a relative volume difference of 1.87±1.39%, an average symmetric surface distance of 0.80±0.23mm, a root mean squared symmetric distance of 1.03±0.33mm and a maximum symmetric surface distance of 4.18±3.45mm. With our method, the capsules of both kidneys are segment in less than 40 seconds.
Uniform patterned synthesis of vertically-aligned carbon nanotubes on low-stress micromechanical structures (2004)

We report a simple methodology to enable the integration of high yield, uniform and preferential growth of vertically-aligned carbon nanotubes (VACNTs) on micromechanical and nanomechanical structures. This technique uses a combination of 'electron beam crosslinked' polymethylmethacrylate (PMMA) surface nanomachining and direct current plasma enhanced chemical vapor deposition (dc-PECVD) of carbon nanotubes.
Learning Inclination to Empathy from Social Media Footprints (2017)

In recent years we are witnessing a growing spread of social media footprints, as the consequence of the wide use of applications such as Facebook, Twitter or LinkedIn, which allow people to share content that might provide information about personal preferences and aptitudes. Among the traits that can be inferred, empathy is the ability to feel and share another person's emotions and we consider it as a relevant aspect for the profiling and recommendation tasks. We propose a method that predicts its level for the user by exploiting her social media data and using linear regression algorithms. The results show which are the most relevant correlations among the different groups of user's features and the empathy level predicted.
Error probability and near-far resistance of minimum mean squared error interference suppression schemes for CDMA (2003)

Interference suppression schemes for direct-sequence spread-spectrum (DS/SS) code division multiple access (CDMA) systems using the minimum mean squared error (MMSE) criterion are considered. When compared to other interference suppression schemes, such as maximum-likelihood decoding, this criterion has the advantage of being amenable to adaptive implementations that do not require knowledge of the interference parameters, such as their relative strengths and spreading sequences. These schemes are shown to be near-far resistant to varying degrees, depending on their complexity. That is, the error probability remains relatively low no matter how strong the interference. Numerical results showing error probability vs. interference power demonstrate that the proposed schemes offer substantial performance gains relative to the matched filter receiver.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Two Serologically Distinguishable Subclasses of µ-Chains of Human Macroglobulins (1967)

Summary One of 16 antisera to pathologic macroglobulins detected serologic differences between them, thus permitting their division into at least two subclasses. Approximately one-third of 40 proteins reacted with this antiserum after it was absorbed with an antigenically deficient protein. The unique determinants were located on the heavy (µ)-chains. Though able to inhibit precipitation of reactive proteins, neither the heavy chains nor the 7 to 8 S monomers from reactive proteins were able to precipitate the absorbed antiserum.
Expression of Mucin‐1 in multiple myeloma and its precursors: correlation with glycosylation and subcellular localization (2013)

Our findings indicate that aberrant glycosylation of MUC1 is an early event in the pathogenesis of MM. In contrast, MUC1C nuclear localization is not likely to be a driver of tumour progression.
REGULATION OF OVARIAN FOLLICLE ATRESIA (1997)

The majority of ovarian follicles undergo atresia, a hormonally controlled apoptotic process. Monitoring apoptotic DNA fragmentation provides a quantitative and sensitive endpoint to study the hormonal regulation of atresia in ovarian follicles. During follicle development, gonadotropins, together with local ovarian growth factors (IGF-I, EGF/TGF-alpha, basic FGF) and cytokine (interleukin-1 beta), as well as estrogens, activate different intracellular pathways to rescue follicles from apoptotic demise. In contrast, TNF-alpha, Fas ligand, presumably acting through receptors with a death domain, and androgens are atretogenic factors. These diverse hormonal signals probably converge on selective intracellular pathways (including genes of the bcl-2 and ICE families) to regulate apoptosis. With a constant loss of follicles from the original stockpile, the ovary provides a unique model for studying the hormonal regulation of apoptosis.
<title>Optimization glitches in zoom lens design</title> (1997)

Various glitches encountered during the optimization of several high performance zoom lenses are described with reference to final lens designs.
OLED microdisplays: a new key element for fringe projection setups (2004)

A new illumination concept for fringe projection will be presented. Up to now fringe projection systems were based on reflective and/or transmissive microdisplays like digital micromirror devices (DMDs), nematic liquid crystals displays (LCDs) or liquid crystal on silicon displays (LCOS). But the size of the light source and of the illumination optic is a strong limitation for the miniaturization of the sensor system itself or for the integration in other illumination setups. Here we propose to use a high-brightness OLED-display (organic light-emitting diode) as active element for fringe pattern generation, giving the possibility to realize compact projection units.
Copy number profiling in von hippel‐lindau disease renal cell carcinoma (2011)

Germline mutations in the VHL tumor suppressor gene cause von Hippel-Lindau (VHL) disease and somatic VHL mutations occur in the majority of clear cell renal cell carcinoma (cRCC). To compare copy number abnormalities (CNAs) between cRCC from VHL patients and sporadic cRCC cases without detectable somatic VHL mutations, we analyzed 34 cRCC with Affymetrix 250K arrays. To increase the power of the study, we then combined our results with those of a previously published study and compared CNAs in VHL and non-VHL related cRCC using the genomic identification of significant targets in cancer (GISTIC) program. In VHL, cRCC GISTIC analysis identified four statistically significant regions of copy number gain and four statistically significant regions of deletion that occurred in >10% of tumors analyzed. Sporadic cRCC without detectable VHL mutations had, on average, more copy number abnormalities than VHL cRCC though the most common regions of loss/gain (e.g., 3p and 14q loss and 5q gain) were present in both tumor sets. However, CNAs on chromosome arms 7p (gain) and 8p (loss) were only detected in VHL RCC. Although individual copy number abnormality peaks contained clear candidate cancer genes in some cases (e.g., the 3p loss peak in VHL cRCC contained only six genes including VHL), most peaks contained many genes. To date, only a minority of the candidate genes included in these peaks have been analyzed for mutation or epigenetic inactivation in cRCC but TNFRSF10C and DUSP4 map to the 8p region deleted in VHL cRCC and TP53 and HIF2A (EPAS1) mapped to CNA loss and gain peaks (chromosomes 17 and 2, respectively) detected in sporadic VHL wild-type cRCC.
Soft-Switching Interleaved PFC Converter with Lossless Snubber (2015)

This paper describes a soft-switching interleaved power factor correction (PFC) converter with a lossless snubber. AC/DC converters require a unity input power factor characteristic with highly efficient operation to prevent the inflow of harmonic current to the power source. The proposed PFC converter improves the input current ripple with interleave control. The converter realizes a high efficiency by the soft-switching operation of all switching devices without a large auxiliary resonant circuit. This paper introduces the soft-switching operation of the converter. In order to confirm the validity of the proposed converter, experiments with a prototype of the PFC converter have been performed. The experimental results indicate that the proposed converter can realize the soft-switching operation of all switching devices, a reduction in the input current ripple, a unity input power factor of 98% or more, a sinusoidal input current, and constant output voltage control. The efficiency of the proposed PFC converter with a lossless snubber is higher than that without the lossless snubber. The results presented in this paper confirm the validity of the proposed converter.
The time reversal kaleidoscope: a new concept of smart transducers for 3D imaging (2004)

The design of two dimensional arrays for real time 3D imaging is a major challenge in medical ultrasound. Several thousand of transducers are typically needed to achieve the beam focusing and steering in a large 3D region of interest. Here we report a completely new approach for producing 3D images with a very small number of transducers using the combined concepts of time reversal mirrors and chaotic reverberating cavities. A small number of transducers glued on the surface of a solid cavity are used in a time reversal mode. If one face of the cavity is in contact with a fluid medium (like the body), ultrasonic waves transmitted by the transducers may take benefit of cavity reverberations to focus in any point of the fluid by using time reversal techniques. Due to the reverberations inside the cavity, waves emitted by each transducer are reflected hundred of times, creating at each reflection 'virtual' transducers that can be observed by any observer located in the fluid. The result of such an operation is that a small number of transducers (typically 32) is multiplied by a number greater than hundred to create a kaleidoscopic transducer array presenting equivalent performances than conventional 2D matrices made of thousands of transducers. The time reversal technique allows us to use these 'virtual' transducers to focus with a very weak side lobe level on each point of the fluid. First experimental 3D images obtained with a pioneer prototype will be presented. Beyond the scope of 3D medical imaging, this combination of time reversal processing with chaotic reverberating cavities leads to the concept of a 'smart' transducer.
FOXQ1 is differentially expressed across breast cancer subtypes and potentially can serve as a prognostic marker (2020)

As a member of the forkhead box (FOX) superfamily of transcription factors, FOXQ1 plays a critical role in a wide range of biological processes, including angiogenesis, epithelial differentiation and smooth muscle differentiation. Emerging evidence also show FOXQ1 to play important roles in the development and progression of various cancers such as ovarian, pancreatic, and colorectal cancer. Particularly, FOXQ1 has been linked to facilitating tumor invasion and metastasis in breast cancer and has also been specifically associated with Triple Negative Basal‐like Breast Cancer (TN/BL BC). Furthermore, experimental studies have demonstrated FOXQ1 overexpression to promote/mediate epithelial to mesenchymal transition, invasion, stemness traits, and chemoresistance in breast cancer. These processes contribute substantially to poor prognosis in breast cancer patients, thus making FOXQ1 a potential target for the diagnosis and treatment of breast cancer tumors. In this study, we investigated the mechanisms leading to increased expression levels of FOXQ1 in BC through analysis of FOXQ1 copy number variation (CNV) and mRNA levels across BC patient subtypes and cell lines. Additionally, we assessed the prognostic significance of FOXQ1 in BC patients. Finally, K‐means clustering was conducted by using Python coding to identify unique clusters for FOXQ1 mRNA levels and CNV in BC cell lines. We report for the first time, that FOXQ1 mRNA is differentially expressed across BC patients. FOXQ1 mRNA is significantly down regulated in Luminal (ER+) BC patients (n=6) when compared to control samples (n=6). FOXQ1mRNA expression is significantly up regulated in TN/BL BC patients (n=6) compared to Her2 (n=6) and ER+ BC (n=6) respectively. We also found FOXQ1 significantly has more copies in TN/BL BC compared to control samples. K‐means clustering analysis was conducted on BC cell lines, with the purpose of identifying distinct subpopulations based on FOXQ1 mRNA expression and CNV. Our supervised and unsupervised clustering analyses identified 3 and 4 clusters, respectively, among BC cell lines for FOXQ1 mRNA compared to their CNV. However, we found FOXQ1 mRNA expression to be independent of its CNV. Moreover, FOXQ1 mRNA was found to be highly expressed in numerous TN/BL cell lines. Lastly and most importantly, by applying the bioinformatic online tool GEPIA, Kaplan‐Meier survival curve analysis identified two risk groups with high (n=524) and low (n=531) FOXQ1 mRNA expression levels. Our Kaplan‐Meier survival analysis also showed patients with low FOXQ1 mRNA expression to have shorter overall survival time than those with high FOXQ1 mRNA expression (HR=0.71, P=0.042). In accordance to these results, we propose that FOXQ1 can serve as an emerging new prognostic biomarker for BC. Understanding the mechanism(s) underlying FOXQ1’s activation in breast cancer could facilitate the development of improved therapies for BC patients. Support or Funding Information Women and Children Health Research Institute Faculty of Medicine and Dentistry, U of A
Structure of the metJBLF cluster in Escherichia coli K12. Sequence of the metB structural gene and of the 5‘- and 3‘-flanking regions of the metBL operon. (1983)

The total nucleotide sequence (1,158 nucleotides) of the metB gene of Escherichia coli coding for cystathionine gamma-synthase (386 amino acid residues, Mr = 41,503/chain) is presented. The nucleotide sequences of the flanking regions of the metB and metL genes are also presented. Analysis of these sequences and identification of a promoter region upstream from the metB gene confirms that metB and metL form an operon. The transcription direction is from metB to metL; the start site of the gene transcription has been determined. There is no structural evidence of a classical attenuation mechanism in the regulation of this operon coding for enzymes implicated in an amino acid biosynthetic pathway. Finally, the overall organization of the metJBLF gene cluster is discussed.
Absorption and Fluorescence Data of Acetone, 3-Pentanone, Biacetyl, and Toluene at Engine-Specific Combinations of Temperature and Pressure (2005)

&lt;div class="htmlview paragraph"&gt;Quantitative planar laser-induced fluorescence measurements of fuel/air mixing in engines are usually based on the use of fluorescence tracers. The strength of the signals often depends on temperature, pressure and mixture composition. This complicates a quantitative analysis. The use of a small-bore optical engine for fundamental studies of absorption and fluorescence properties of fluorescence tracers is described. The temperature, pressure and composition dependence of the spectra of toluene, acetone, 3-pentanone, and biacetyl are examined under motored conditions to extend the experimental data base for the development of comprehensive models that predict the strength of fluorescence signals for a given condition.&lt;/div&gt;