gebhart/patrepeval huggingface dataset:
3D Statistical Shape Models of Patella for Sex Classification (2006)

This paper proposes a new sex classification method from patellae using a novel automated feature extraction technique. A dataset of 228 patellae (95 females and 133 males) was collected and CT scanned. After the CT data was segmented, a set of features was automatically extracted, normalized, and ranked. These features include geometric features, moments, principal axes, and principal components. A feature vector of 45 dimensions for each subject was then constructed. A set of statistical and supervised neural network classification methods were used to classify the patellar feature vectors according to sex. Different classification methods were compared. Classification success ranged from 83.77% average classification rate with labeling using fuzzy C-Means method (FCM), to 90.3% for linear discriminant function (LDF) analysis. We obtained results of 96.02% and 93.51% training and testing classification rates (respectively) using feedforward backpropagation Neural Networks (NN). These promising results encourage the usage of this method in forensic anthropology for identifying the sex from incomplete skeletons containing at least one patella.
Abstract 166 (2014)

AMERICAN SOCIETY OF PLASTIC SURGEONS PLASTIC & RECONSTRUCTIVE SURGERY PRS GLOBAL OPEN ASPS EDUCATION NETWORK AMERICAN SOCIETY OF PLASTIC SURGEONS PLASTIC & RECONSTRUCTIVE SURGERY PRS GLOBAL OPEN ASPS EDUCATION NETWORK
Table S2 from Chemogenomic Landscape of <i>RUNX1</i>-mutated AML Reveals Importance of <i>RUNX1</i> Allele Dosage in Genetics and Glucocorticoid Sensitivity (2023)

&lt;p&gt;RUNX1 mutations identified in the Leucegene cohort. Position of mutations are indicated using NM_001754 and NM_001001890, coding for RUNX1 proteins of 480 and 453 AA respectively. VAF: variant allele frequency.&lt;/p&gt;
A wideband statistical model for NLOS indoor MIMO channels (2003)

Herein, results of 5.2 GHz wideband indoor multiple input multiple output (MIMO) channel measurements under the EU IST SATURN project are reported. Our investigation shows that for non-line-of-sight (NLOS) cases, the average power delay profiles fit the exponentially decaying curve quite well, therefore a simple wideband model for single-input single-output (SISO) proposed in COST259 has been used in our model. Furthermore, the investigations show that the MIMO channel covariance matrix of each normalized tap of the impulse response could be well approximated by the Kronecker product of the covariance matrices seen from the transmitter and receiver respectively. Based on the above results, a wideband statistical model is presented. Monte-Carlo simulations show reasonably good agreement between the measured data and our model. Finally, we use this model to show some capacity characteristics of Hiper-LAN/2 channels in NLOS indoor scenarios.
Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs (2020)

Proteins often have both orthosteric and allosteric binding sites. Endogenous ligands, such as hormones and neurotransmitters, bind to the orthosteric site, while synthetic ligands may bind to orthosteric or allosteric sites, which has become a focal point in drug discovery. Usually, such allosteric modulators bind to a protein noncompetitively with its endogenous ligand or substrate. The growing interest in allosteric modulators has resulted in a substantial increase of these entities and their features such as binding data in chemical libraries and databases. Although this data surge fuels research focused on allosteric modulators, binding data is unfortunately not always clearly indicated as being allosteric or orthosteric. Therefore, allosteric binding data is difficult to retrieve from databases that contain a mixture of allosteric and orthosteric compounds. This decreases model performance when statistical methods, such as machine learning models, are applied. In previous work we generated an allosteric data subset of ChEMBL release 14. In the current study an improved text mining approach is used to retrieve the allosteric and orthosteric binding types from the literature in ChEMBL release 22. Moreover, convolutional deep neural networks were constructed to predict the binding types of compounds for class A G protein-coupled receptors (GPCRs). Temporal split validation showed the model predictiveness with Matthews correlation coefficient (MCC) = 0.54, sensitivity allosteric = 0.54, and sensitivity orthosteric = 0.94. Finally, this study shows that the inclusion of accurate binding types increases binding predictions by including them as descriptor (MCC = 0.27 improved to MCC = 0.34; validated for class A GPCRs, trained on all GPCRs). Although the focus of this study is mainly on class A GPCRs, binding types for all protein classes in ChEMBL were obtained and explored. The data set is included as a supplement to this study, allowing the reader to select the compounds and binding types of interest.
Gap-junction communication between autologous endothelial and tumor cells induce cross-recognition and elimination by specific CTL (41.58) (2009)

Abstract Cellular interactions in the tumor stroma play a major role in cancer progression but can also induce tumor rejection. To explore the role of endothelial cells in these interactions, we used an in vitro 3D collagen matrix model containing a cytotoxic T lymphocyte CTL clone (M4.48), autologous tumor cells (M4T) and an endothelial cell (M4E) line that are all derived from the same tumor. We demonstrate here that specific killing of the endothelial cells by the CTL clone required the autologous tumor cells and involved antigen cross-presentation. The formation of gap-junctions between endothelial and tumor cells is required for antigenic peptide transfer to endothelial cells that are then recognized and eliminated by CTL. Our results indicate that gap-junctions facilitate an effective CTL-mediated destruction of endothelial cells from the tumor microenvironment which may contribute to the control of tumor progression.
Salted mesostructures: salt-liquid crystal templating of lithium triflate-oligo(ethylene oxide) surfactant-mesoporous silica nanocomposite films and monoliths (1999)

A lyotropic lithium triflate-silicate liquid crystal is utilized as a supramolecular template for a ‘one-pot’ synthesis of a novel ionically conducting nanocomposite material, denoted meso-SiO 2 -C 12 (EO) 10 OH-LiCF 3 SO 3 , in the form of a film or monolith. In this structure Li + ions interact, in a crown ether-like fashion, with oligo(ethylene oxide) head groups of a non-ionic surfactant assembly that is imbibed within the channels of hexagonal mesoporous silica. Details of the acid catalyzed polymerization of the silicate oligo(ethylene oxide) surfactant co-assembly in the presence of lithium triflate have been investigated using polarized optical microscopy (POM), powder X-ray diffraction (PXRD), multinuclear nuclear magnetic resonance (NMR) spectroscopy and impedance spectroscopy. Insight into the incorporation of Li + and CF 3 SO 3 – ions into meso-SiO 2 -C 12 (EO) 10 OH-LiCF 3 SO 3 was obtained using NMR and Fourier transform (FT) Raman spectroscopy. Collectively the results indicate that lithium ions coordinate to oxygens of the oligo(ethylene oxide) head group, maintain the structural integrity of both the silicate liquid crystal and templated mesoporous silica, and are essentially completely dissociated with respect to the triflate counteranion. ac Impedance spectroscopy, which bodes well for their use in the fields of polymer electrolytes and battery technology for meso-SiO 2 -C 12 (EO) 10 OH-LiCF 3 SO 3 have demonstrated high ionic conductivities at room temperature measurements. Salt-liquid crystal templating may offer a general approach for synthesizing diverse kinds of salted mesostructures including redox active transition metal complexes, which may be reductively-agglomerated to form metal cluster-based meso-SiO 2 -C 12 (EO) 10 OH-M n or sulfided with H 2 S to produce semiconductor cluster-based meso-SiO 2 -C 12 (EO) 10 OH-(MS) n nanocomposites.
Cholesterol levels and plasma membrane fluidity in 3T3 and SV101‐3T3 cells (1979)

Polyene antibiotics such as filipin selectively inhibit wheat germ agglutinin-induced agglutination of transformed and malignant cells compared to normal cells (Hatten ME, Burger MM: Biochemistry 18: 739, 1979). Since filipin binds specifically to cholesterol, we measured cholesterol levels in 3T3 cells and SV101-3T3 cells. SV101-3T3 cells contained 50-100% more cholesterol per cell than 3T3 cells. Both cell types were starved for cholesterol by growth in lipid-depleted medium plus 25-hydroxycholesterol. The cholesterol level of SV101-3T3 cells decreased by 30-50%, while the level in 3T3 cells remained constant. Filipin-stained SV101-3T3 cells revealed bright patches of filipin under fluorescence microscopy. These patches were absent in 3T3 cells and in SV101-3T3 and 3T3 cells starved for cholesterol. We selectively labeled plasma membranes of these cells with a spin label analog of phosphatidylcholine. The spin label indicated differences in plasma membrane fluidity that may be related to the different cholesterol levels in 3T3 and SV101-3T3 cells.
Surviving the host: Microbial metabolic genes required for growth of Pseudomonas aeruginosa in physiologically-relevant conditions (2022)

<i>Pseudomonas aeruginosa,</i> like other pathogens, adapts to the limiting nutritional environment of the host by altering patterns of gene expression and utilizing alternative pathways required for survival. Understanding the genes essential for survival in the host gives insight into pathways that this organism requires during infection and has the potential to identify better ways to treat infections. Here, we used a saturated transposon insertion mutant pool of <i>P. aeruginosa</i> strain PAO1 and transposon insertion sequencing (Tn-Seq), to identify genes conditionally important for survival under conditions mimicking the environment of a nosocomial infection. Conditions tested included tissue culture medium with and without human serum, a murine abscess model, and a human skin organoid model. Genes known to be upregulated during infections, as well as those involved in nucleotide metabolism, and cobalamin (vitamin B<sub>12</sub>) biosynthesis, etc., were required for survival <i>in vivo</i>- and in host mimicking conditions, but not in nutrient rich lab medium, Mueller Hinton broth (MHB). Correspondingly, mutants in genes encoding proteins of nucleotide and cobalamin metabolism pathways were shown to have growth defects under physiologically-relevant media conditions, <i>in vivo, and in vivo-</i>like models, and were downregulated in expression under these conditions, when compared to MHB. This study provides evidence for the relevance of studying <i>P. aeruginosa</i> fitness in physiologically-relevant host mimicking conditions and identified metabolic pathways that represent potential novel targets for alternative therapies.
Positive regulation of pertussis toxin expression. (1988)

Although the genus Bordetella contains several closely related species, pertussis toxin (PT) is produced only by phase I Bordetella pertussis. In this work we have studied the regulation of expression of the PT operon and investigated why PT is produced by phase I and not by phase III B. pertussis despite the presence of the PT genes. We have constructed a vector for Bordetella species that contains the PT promoter fused to the coding region of the chloramphenicol acetyltransferase (CAT) gene, and we have used it to identify the regulatory elements involved in the transcription of the PT operon. Efficient transcription of these genes requires at least two features: (i) the 170-base-pair DNA sequence upstream from the start site of transcription and (ii) a trans-activating factor encoded by the vir locus. Bordetella parapertussis and Bordetella bronchiseptica, although endowed with a functional trans-activating system, do not produce PT because of mutations within their PT promoter regions. In contrast, phase III Bordetella species do not show any trans activity.
Performance characteristics of continuously grated multicore sensor fiber (2017)

We describe the fabrication and performance of a continuously grated twisted multicore fiber sensor array. The grated fiber sensor comprises nearly continuous Bragg gratings along its entire length. The gratings are inscribed over lengths in excess of 10m in fibers with UV transparent coating using a flexible and scalable reel to reel processing system. The arrays are tested using optical frequency domain reflectometry (OFDR). We report on automated analysis routines applied to these OFDR measurements that allow for characterization of 100s of individual grating exposures that make up a continuously grated fiber length. We also report on the spectral loss of the continuously grated fiber, showing that it is suitable for applications with sensors in excess of 100m. Finally, we report on the fiber sensing characteristics by performing measurements of fiber bend using a fiber shape reconstruction algorithm on OFDR traces obtained from four of the fiber cores.
Renal Cell Carcinoma (RCC) Tumors Display Large Expansion of Double Positive (DP) CD4+CD8+ T Cells With Expression of Exhaustion Markers (2018)

Checkpoint inhibitors target the inhibitory receptors expressed by tumor-infiltrating T cells in order to reinvigorate an anti-tumor immune response. Therefore, understanding T cell composition and phenotype in human tumors is crucial. We analyzed by flow cytometry tumor-infiltrating lymphocytes (TILs) from two independent cohorts of patients with different cancer types, including RCC, lung, and colon cancer. In healthy donors, peripheral T cells are usually either CD4+ or CD8+ with a small percentage of CD4+ CD8+ DP cells (<5%). Compared to several other cancer types, including lung, and colorectal cancers, TILs from about a third of RCC patients showed an increased proportion of DP CD4+CD8+ T cells (>5%, reaching 30-50% of T cells in some patients). These DP T cells have an effector memory phenotype and express CD38, 4-1BB, and HLA-DR, suggesting antigen-driven expansion. In fact, TCR sequencing analysis revealed a high degree of clonality in DP T cells. Additionally, there were high levels of PD-1 and TIM-3 expression on DP T cells, which correlated with higher expression of PD-1 and TIM-3 in conventional single positive CD8 T cells from the same patients. These results suggest that DP T cells could be dysfunctional tumor-specific T cells with the potential to be reactivated by checkpoint inhibitors.
A 6.8mW 7.4Gb/s clock-forwarded receiver with up to 300MHz jitter tracking in 65nm CMOS (2010)

The clock path in a 65 nm CMOS receiver comprises two injection-locked oscillators to frequency-multiply, deskew, and track correlated jitter on a pulsed clock forwarded from the transmitter. Latency mismatch and data rates are accommodated by controlling jitter tracking up to 300 MHz. Each receiver consumes 0.92 pJ/b at 7.4 Gb/s with a jitter tolerance of 1.5UI at 200 MHz.
Effect of Estrogen on Musculoskeletal Performance and Injury Risk (2019)

Estrogen has a dramatic effect on musculoskeletal function. Beyond the known relationship between estrogen and bone, it directly affects the structure and function of other musculoskeletal tissues such as muscle, tendon, and ligament. In these other musculoskeletal tissues, estrogen improves muscle mass and strength, and increases the collagen content of connective tissues. However, unlike bone and muscle where estrogen improves function, in tendons and ligaments estrogen decreases stiffness, and this directly affects performance and injury rates. High estrogen levels can decrease power and performance and make women more prone for catastrophic ligament injury. The goal of the current work is to review the research that forms the basis of our understanding how estrogen affects muscle, tendon, and ligament and how hormonal manipulation can be used to optimize performance and promote female participation in an active lifestyle at any age.
Maximizing the bandwidth while minimizing the spectral fluctuations using supercontinuum generation in photonic crystal chalcogenide fibers (2015)

Supercontinuum generation in the mid-infrared (mid-IR) spectrum has a broad array of potential applications in medicine, environmental sensing, and defense. Mid-IR sources play a crucial role in defending aircraft against missile attacks [1]. It is desirable to have a source that acts like a mid-IR “light bulb” to produce a broadband, flat, and incoherent spectrum. In work to date, we have demonstrated that it is possible to obtain a bandwidth of 4 μm in As <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Se <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> chalcogenide hexagonal photonic crystal fibers that are pumped at 2.5 μm with pulse durations that are 500 fs or longer and pump peak powers of 1 kW or more with careful design of the fiber parameters [2]. We have also shown that it is possible to put more than 25% of the power in the range of 3-5 μm in As <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> chalcogenide fibers with a pump at 2 μm [3].
40MHz pulse train based on a temporally demultiplexed 2.56GHz SCOWA low noise mode-locked laser (2008)

An alternative to the sub-100 MHz repetition rate laser source is explored. A low noise SCOWA-based harmonically mode-locked laser is developed and temporally demultiplexed to twice the cavity fundamental resulting in a 40 MHz pulse train.
An experimental and anaiytical investigation of the large strain compressive and tensile response of glassy polymers (1990)

Abstract In this investigation, the plastic flow of polycarbonate (PC) was examined by obtaining true stress‐strain data over a range of strain rates at room temperature through homogeneous, uniaxial, constant strain rate compression testing to strains as high as 125 percent. Uniaxial compressive loading conditions give rise to a planar molecular orientation process which results in the observed strain hardening in compression. Uniaxial tensile tests on PC were also conducted. The necked region of the tensile specimen is being cold drawn resulting in a uniaxial state of orientation. Therefore, the observed macroscopic strain hardening in uniaxial tension distinctly differs from that obtained In uniaxial compression, giving different stress‐strain curves. The major differences experimentally obtained between the large strain response in compression and tension indicate a need for an orientation‐based model of the strain hardening process. The experimental program also acts to uncouple the effects of strain softening and strain rate providing more accurate data for future modeling of the true strain softening process. A constitutive law which directly relates the strain hardening response to the state of molecular network stretch in the polymer is used to model and analyze the experiments. The model is found to simulate the observed rate dependent yield and post yield strain softening and hardening of the compressive data over the entire range of strain rates very well. The model is then utilized in a finite element analysis of the tensile tests on PC. Numerical results compared favorably with the experimental data including: load vs , contraction curves, natural draw ratio, and the axial stress‐strain response of the cold drawing region.
A data mining methodology and its application to semi-automatic knowledge acquisition (2002)

We introduce a methodology for knowledge discovery in databases (KDD) where one first discovers large collections of patterns at once, and then performs interactively retrieves subsets of the collection of patterns. The proposed methodology suits such KDD formalisms as association and episode rules, where large collections of potentially interesting rules can be found efficiently. We present methods that support interactive exploration of large collections of rules. With these methods the user can flexibly specify the focus of interest, and also iteratively refine it. We have implemented our methodology in the TASA system which discovers patterns in telecommunication alarm databases. We give concrete examples of how to use frequent patterns in the construction of alarm correlation expert systems.
ChemInform Abstract: Formation of Copper Thin Films by a Low Kinetic Energy Particle Process. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A hypothesis for temporal coding of young and mature granule cells (2013)

While it has been hypothesized that adult neurogenesis (NG) plays a role in the encoding of temporal information at long time-scales, the temporal relationship of immature cells to the highly rhythmic network activity of the hippocampus has been largely unexplored. Here, we present a theory for how the activity of immature adult-born granule cells relates to hippocampal oscillations. Our hypothesis is that theta rhythmic (5-10 Hz) excitatory and inhibitory inputs into the hippocampus could differentially affect young and mature granule cells due to differences in intrinsic physiology and synaptic inhibition between the two cell populations. Consequently, immature cell activity may occur at broader ranges of theta phase than the activity of their mature counterparts. We describe how this differential influence on young and mature granule cells could separate the activity of differently aged neurons in a temporal coding regime. Notably, this process could have considerable implications on how the downstream CA3 region interprets the information conveyed by young and mature granule cells. To begin to investigate the phasic behavior of granule cells, we analyzed in vivo recordings of the rat dentate gyrus (DG), observing that the temporal behavior of granule cells with respect to the theta rhythm is different between rats with normal and impaired levels of NG. Specifically, in control animals, granule cells exhibit both strong and weak coupling to the phase of the theta rhythm. In contrast, the distribution of phase relationships in NG-impaired rats is shifted such that they are significantly stronger. These preliminary data support our hypothesis that immature neurons could distinctly affect the temporal dynamics of hippocampal encoding.