gebhart/patrepeval huggingface dataset:
Supplementary figure 3 from Abscopal Effects of Radiotherapy Are Enhanced by Combined Immunostimulatory mAbs and Are Dependent on CD8 T Cells and Crosspriming (2023)

&lt;p&gt;Radiotherapy reduced the density and absolute numbers of CD4+, CD8+ and CD25+FOXP3+ T cells and Myeloid-derived suppressor cells both in the irradiated and non-irradiated lesions.&lt;/p&gt;
Memory-centric neuromorphic computing for unstructured data processing (2021)

The unstructured data such as visual information, natural language, and human behaviors opens up a wide array of opportunities in the field of artificial intelligence (AI). The memory-centric neuromorphic computing (MNC) has been proposed for the efficient processing of unstructured data, bypassing the von Neumann bottleneck of current computing architecture. The development of MNC would provide massively parallel processing of unstructured data, realizing the cognitive AI in edge and wearable systems. In this review, recent advances in memory-centric neuromorphic devices are discussed in terms of emerging nonvolatile memories, volatile switches, synaptic plasticity, neuronal models, and memristive neural network.
Adenosine Triphosphate (ATP) Concentrations and ATP/Adenosine Diphosphate Ratios in Human Sperm of Normospermic, Oligospermic, and Asthenospermic Specimens and in their Swim‐up Fractions: Lack of Correlation Between ATP Parameters and Sperm Creatine Kinase Concentrations (1992)

The authors had previously found an inverse correlation between per sperm creatine phosphokinase activity and sperm concentrations in men. Because creatine phosphokinase is a key enzyme in sperm energy transport, the possible relationship of sperm creatine phosphokinase activity, sperm adenosine triphosphate (ATP) concentrations, sperm ATP/ADP (adenosine diphosphate) ratios, and computer-aided semen analysis sperm motility parameters were then studied. The ATP concentrations and ATP/ADP ratios, measured by high-pressure liquid chromatography in washed sperm, were similar in normospermic and oligospermic specimens (ATP: 123.1 +/- 21.6 vs. 90.0 +/- 24.5 pmol/10(6) sperm; ATP/ADP: 2.8 +/- 0.4 vs. 2.1 +/- 0.4, N = 32 and 17, mean +/- SEM), and in samples with normal and less than 40% sperm motility (ATP: 96.8 +/- 27.2 vs. 122.2 +/- 19.6 pmol/10(6) sperm; ATP/ADP: 2.4 +/- 0.5 vs. 2.8 +/- 0.4, n = 26 and 23). In the swim-up sperm fractions, which showed improved motility, the ATP concentrations, but not the ATP/ADP ratios, were lower than in the initial semen samples (ATP: 152.9 +/- 28.4 vs. 90.3 +/- 10.6 pmol/10(6) sperm, P less than 0.05; ATP/ADP: 3.3 +/- 0.5 vs. 3.9 +/- 0.7, N = 18 pairs of samples). This is consistent with our previous finding of a lower cytoplasmic content in sperm in swim-up fractions.(ABSTRACT TRUNCATED AT 250 WORDS)
Tracking bad apples (2007)

Programs sometimes crash due to unusable values, for example, when Java and C# programs dereference null pointers and when C and C++ programs use undefined values to affect program behavior. A stack trace produced on such a crash identifies the effect of the unusable value, not its cause, and is often not much help to the programmer.
Role of NPR1 dependent and NPR1 independent genes in response to Salicylic acid (2017)

NPR1 (Nonexpressor of pathogenesis-related gene) is a transcription coactivator and central regulator of systemic acquired resistance (SAR) pathway. It controls wide range of pathogenesis related genes involved in various defense responses, acts by sensing SAR signal molecule, Salicylic acid (SA). Mutation in NPR1 results in increased susceptibility to pathogen infection and less expression of pathogenesis related genes. The present study aimed to identify the role of NPR1 in gene expression after the Salicylic acid induction. For this RNA-seq was performed in Arabidopsis thaliana Col-0 and npr1-1 in response to Salicylic acid. RNA-seq analysis revealed a total of 3811 differentially expressed gene in which 2109 genes are up-regulated and 1702 genes are down-regulated. We have divided these genes in 6 categories SA induced (SI), SA repressed (SR), NPR1 dependent SI (ND-SI), NPR1 dependent SR (ND-SR), NPR1 independent SI (NI-SI), NPR1 independent SR (NI-SR). Further, Gene ontology and MapMan pathway analysis of differentially expressed genes suggested variety of biological processes and metabolic pathways that are enriched during SAR defense pathway. These results contribute to shed light on importance of both NPR1-dependent (ND) and NPR1-independent (NI) gene acting downstream to Salicylic acid induction in SAR pathway. The present study aimed to identify the role of NPR1 in gene expression after the Salicylic acid induction.
REDESIGNING PLANTS FOR SPACEFLIGHT AND BEYOND: TRANSFER OF GENES FROM PYROCOCCUS (2010)

While much progress has been made in designing
biospheres for optimal plant growth and long term habitation in space, plant productivity remains a major
limiting factor for sustainable bioregenerative life support. To meet these challenges, we propose that plant biologists should work with engineers to redesign plants. For example, the mechanisms that plants engage to sense environmental cues can be replaced or modified to eliminate Earth-based responses no longer needed in space and to add responses that will improve growth in a biosphere. In addition, synthetic approaches can be used to fine tune plant responses to stress by expressing genes from organisms that thrive in extreme environments. Producing extremophilic proteins in crop plants can increase a plant’s tolerance to rapid changes in temperature and improve growth in environments which might otherwise be sensed as stressful. Future efforts to redesign plants provide unlimited promise for developing sustainable bioregenerative life support systems and will lead to new fundamental insights into the regulation of plant growth and development.
ChemInform Abstract: Flow Chemistry — A Key Enabling Technology for (Multistep) Organic Synthesis (2012)

Abstract Review: mainly presented for heterocyclic systems including drug development; ca. 150 refs.
Social construction of home- return of minority refugees (2011)

Konceptualno rad prezentira cetri pristupa povratku manjinskih izbjeglica i njihov 'dom': a)tradicionalni koncepti, kritika tradicionalnih koncepata, novi koncepti povratka i doma (transnacionalizam), kritika novih (postmodernih koncepata povratka i doma. K tome se referat oslanja na reprezentativno nacionalno istraživanje manjinskoga (srpskog) povratka u Hrvatsku, koga su autori proveli za UNHCR.
Scalable representations of diseases in biomedical ontologies (2011)

We defend a judicious use of disjunctive, and therefore ambiguous, classes in biomedical ontologies during the process of ontology construction and in the practice of ontology application. The use of these classes is permitted to span across several top-level categories, provided it contributes to ontology simplification and supports the intended reasoning scenarios.
Quantitative Analysis of Growth Factor Receptor Signaling (2010)

Cell-cell communication and the regulation of cell growth, differentiation and death are primarily mediated by an array of secreted cytokines and growth factors acting through a large class of multi-component cell-surface receptors. Our quantitative understanding of how these receptors function remains rudimentary, however, providing an obstacle to achieving a quantitative, systems-level description of many critical cellular processes. In this presentation I will describe our work on the activation and signaling mechanism of the RET tyrosine kinase receptor. Specifically, I will describe how we have established the sequence of steps by which the binding of ligand leads to assembly of the activated RET receptor complex on cells, how assembly of the activated receptor complex is quantitatively coupled to proximal and distal steps in intracellular signaling, and what we have learned concerning how biochemical mechanism drives biological function in this and related receptor systems.
JOINT PROCESSING OF FORWARD AND BACKWARD EXTENDED PRONY AND WEIGHTED SPECTRAL SEMBLANCE METHODS FOR ROBUST EXTRACTION OF VELOCITY DISPERSION DATA (2010)

Various extensions of the Prony method are commonly used to detect and extract frequency-slowness disper- sion data from array sonic waveforms. We introduce a new dispersion method that combines the forward and backward extended Prony method with the weighted spectral semblance method to improve slowness disper- sion estimation from waveforms with presence of noise. The procedure works as follows: (1) the forward and backward extended Prony method is used to find the poles of the associated characteristic polynomials and to reconstruct the array waveform data; (2) the 2D ma- trix of weights is calculated in the frequency-slowness plane according to the slownesses associated with the poles; and (3) the correlation matrix is calculated using weighted spectral semblance, wherein the 2D weight matrix is included. The new method is applied to noisy sonic logging field data. Results show that estimation of dispersion curves using the new method is more robust than those ob- tained with either the backward (or forward) extended Prony method or the weighted spectral semblance method. Our method also outperforms alternative, commonly used approaches in the elimination of alias- ing effects.
Patología escapular en pediatría (2012)

Poster: SERAM 2012 / S-1543 / Patologia escapular en pediatria by: E. Garcia Esparza, I. Solis Muniz, M. A. Lopez Pino, S. I. Sirvent, G. Albi, G. Gomez Mardones; Madrid/ES
Efficacy of UV irradiation on eight species of <i>Bacillus</i> (2006)

Ultraviolet irradiation has commonly been used in the indoor environment to eliminate or control infectious diseases such as tuberculosis in medical care facilities. Heating, ventilating, and air-conditioning (HVAC) system components such as duct-liners, cooling coils, drip-pans, interior insulation, and areas subjected to high levels of moisture can create an environment that is prone to biological contamination. Air supplied to indoor environments can carry biological contaminants that can expose numerous building occupants to pathogenic organisms. Possible terrorist activities could release biological agents into ambient air, or directly into a building environment, or HVAC system may expose multitudes of individuals to dangerous pathogens. The use of germicidal ultraviolet lamps (UVGI) in commercial and residential HVAC systems has increased. A method to determine the antimicrobial efficacy of UVGI irradiation was developed and tested on the surface of agar plates with eight varieties of Bacillus bacteria spores. Bacillus anthracis surrogates were used for their expected similar inactivation responses to UVGI irradiation. The percent kill and k value for each organism was calculated for various periods of exposure.Key words: antimicrobial, germicidal, antimicrobial efficacy, HVAC, biocontaminant.
Measurement of orientation and susceptibility ratios using a polarization-resolved second-harmonic generation holographic microscope (2012)

Three-dimensional second-harmonic fields, sample orientation, and susceptibility ratios of biological samples are measured using polarization-resolved second-harmonic generation (SHG) microscopy. The three-dimensional (3D) polarization is gathered by measurement of a series of holograms for which excitation and analyzer polarizations are systematically varied, and the 3D SHG field is recovered through numerical back propagation. Harmonophore orientation is resolved in 3D from a sub-set of polarization-resolved SHG holograms. We further expand on previous approaches for the determination of susceptibility ratios, adding the calculation of multiple ratio values to allow intrinsic verification.
Calculation of Thermodynamic and Structural Characteristics of Gold and Silver Solvate Complexes (2020)

Gold and silver complexes with cyanide, thiocyanate, and thiosulfate ions have been considered. The potential energy surfaces of sorption complexes are shown. Quantum-chemical calculations of gold and silver complexes have been performed by the PM6 semi-empirical method as part of MOPAC. For eleven gold compounds, sets of potential energies have been obtained for various combinations. The potential energies for silver complexes have been calculated. As a result, data on the behavior of complex ions during sorption on anion exchange resin, the presence of energy minima, the pathways of the reaction, more accurate values of the binding energy, or the absence of sorption interaction in the system have been refined. Consideration of the sorption of gold and silver complexes from the classical standpoint of chemical kinetics made it possible to evaluate the activation energy and the nature of the interaction during the process. The thermodynamic parameters of the studied chemical processes have been calculated.
Supplemental Table 12 from Expression of &lt;i&gt;ANRIL&lt;/i&gt;–Polycomb Complexes–&lt;i&gt;CDKN2A/B/ARF&lt;/i&gt; Genes in Breast Tumors: Identification of a Two-Gene (&lt;i&gt;EZH2/CBX7&lt;/i&gt;) Signature with Independent Prognostic Value (2023)

&lt;p&gt;Relationship between P15 transcripts levels and classical clinical biological parameters in a series of 456 breast cancers.&lt;/p&gt;
Coexpression of CCR7 and CXCR4 during B cell development controls CXCR4 responsiveness and bone marrow homing (2019)

Abstract G protein-coupled receptors (GPCR) constitute the largest family of plasma membrane proteins involved in cell signaling. Besides their canonical role in signaling, GPCR can also act as allosteric modulator of one another through receptor oligomerization. However, only few studies have investigated the relevance of GPCR oligomerization, and the role of GPCR interaction in physiological processes remains largely unknown. By using chemokine receptors and B cell development as a model system, we unveil in this study a novel role for CCR7 as a selective endogenous allosteric modulator of CXCR4. We show that the upregulation of CCR7 expression naturally occurring in late stages of B cell development contributes to the functional inactivation of CXCR4, and that B cell populations from CCR7 -/- mice display higher responsiveness to CXCL12 and improved retention in the bone marrow parenchyma. We also provide molecular evidences supporting a model in which upregulation of CCR7 favors the formation of CXCR4-CCR7 heteromers wherein CXCR4 is selectively impaired in its ability to activate some G protein complexes.
Racial Differences in Growth Patterns of Children Assessed on the Basis of Bone Age (2008)

Ethnic and racial differences in growth patterns exist at certain ages; however, the Greulich and Pyle atlas does not recognize this fact. Assessment of bone age in children with use of the Greulich and Pyle atlas can be improved by considering the subject's ethnicity.
Ultralow chromatic dispersion measurement of optical fibers with a tunable fiber laser (2006)

We describe a novel convenient technique to allow for the accurate measurement of the dispersion coefficients till fourth-order in the zero-dispersion wavelength region of single-mode optical fibers. The proposed method is based on a careful spectral analysis of modulation instability occurring in both normal and anomalous dispersion regime and the associated dispersive waves emitted by soliton fission. It simply requires a high-power tunable continuous-wave fiber laser and an optical spectrum analyzer and is able to retrieve both the sign and magnitude of dispersion coefficients with enhanced precision
Self‐Assembled Nanoparticles Based Fabrication of Gecko Foot‐Hair‐Inspired Polymer Nanofibers (2007)

Abstract Wafer‐scale polymer nanofabrillar structures have been fabricated using the combination of colloidal nanolithography, deep‐silicon etching, and nanomolding to mimic the nanostructure of gecko foot‐hairs. The artificial surface features densely packed polymeric nanofibrils with super‐hydrophobic, water‐repellent, and “easy‐to‐clean” characteristics. The lateral dimension of the nanofibrils is as small as 250 nm and an aspect‐ratio as high as 10:1 has been achieved without lateral collapse between neighboring fibrils. The method allows both fabrication of synthetic structures over a large area and direct integration of a flexible membrane to assist the array of nanofibrils in making intimate contact with uneven surfaces. A single nanofibril exhibits a mean adhesive force ranging from (0.91 ± 0.34) nN to (1.35 ± 0.37) nN. In the macroscopic scale, the nanostructured surface can adhere firmly to a smooth glass substrate and inherits the in‐use, self‐cleaning property of the setal nanostructures found in gecko lamellae.
Pulsed OPO brightness improvement by means of intracavity spatial filtering (1999)

International audience
Distal femur varus-producing osteotomy: An updated review of patellofemoral implications and clinical outcomes (2023)

Background: Recent evidence seems to suggest the effectiveness of distal femur varus osteotomy in the management of patellofemoral instability in the setting of genu valgum. However, literature on this subject remains scarce and consists mostly of small case series. Hypothesis: This study aims to systematically review the literature on varus-producing distal femur osteotomy and critically analyze its implications on patellofemoral kinematics and stability. Results: The statistical analysis revealed that this surgery is able to restore a mechanical angle (mean hip–knee–ankle (HKA): 0.22°) and to improve the main clinical outcomes (Kujala score, Knee injury and Osteoarthritis Outcome Score, visual analog scale) after a mean follow up of 2.5 years. An objective of the present review was to investigate the mechanical implications of femoral osteotomy on the patellofemoral biomechanics. Indeed, the statistical analysis demonstrated changes after surgery in the main patella-femoral radiological angles (modified Insall–Salvati index, Caton–Deschamps index, Blackburne–Peel index). Interestingly the overcorrection of the mechanical axis (HKA), resulting in varus, had similar outcomes compared to studies that obtained a mechanical axis. Level of Evidence: Level II study.
Preparation of Aroyl and Arenesulfonyl Fluorides from the Corresponding Chlorides Using Zinc Fluoride–Pyridine System (1978)

Abstract Convenient preparation of aroyl and arenesulfonyl fluorides in high yields was achieved by the reaction of the corresponding chlorides with zinc fluoride in pyridine.
Controlled Sub‐Micrometer Hierarchical Textures Engineered in Polymeric Fibers and Microchannels via Thermal Drawing (2017)

The controlled texturing of surfaces at the micro‐ and nanoscales is a powerful method for tailoring how materials interact with liquids, electromagnetic waves, or biological tissues. The increasing scientific and technological interest in advanced fibers and fabrics has triggered a strong motivation for leveraging the use of textures on fiber surfaces. Thus far however, fiber‐processing techniques have exhibited an inherent limitation due to the smoothing out of surface textures by polymer reflow, restricting achievable feature sizes. In this article, a theoretical framework is established from which a strategy is developed to reduce the surface tension of the textured polymer, thus drastically slowing down thermal reflow. With this approach the fabrication of potentially kilometers‐long polymer fibers with controlled hierarchical surface textures of unprecedented complexity and with feature sizes down to a few hundreds of nanometers is demonstrated, two orders of magnitude below current configurations. Using such fibers as molds, 3D microchannels are also fabricated with textured inner surfaces within soft polymers such as poly(dimethylsiloxane), at dimensions and a degree of simplicity impossible to reach with current techniques. This strategy for the texturing of high curvature surfaces opens novel opportunities in bioengineering, regenerative scaffolds, microfluidics, and smart textiles.
Structuring of carbon nanotubes for field emission based movement sensors (2012)

This paper addresses the exploitation of the field emitting properties of carbon nanotubes for movement sensor applications. To utilize this transducer principle a well defined gap between the field emitting carbon nanotubes and the counter electrode must be formed. Three different methods to dissect the dielectrophoretically deposited carbon nanotubes in a reproducible way are presented.
Supplemental Figure S5 from Loss of &lt;i&gt;ARID1A&lt;/i&gt; Activates &lt;i&gt;ANXA1&lt;/i&gt;, which Serves as a Predictive Biomarker for Trastuzumab Resistance (2023)

&lt;p&gt;Supplemental Figure S5: METABRIC Boxplot and survival figures&lt;/p&gt;
Optimized integrated copper gap-fill approaches for 2x flash devices (2009)

Physical vapor deposited (PVD) Cu seed layers have been successfully implemented for Cu gap-fill in feature sizes for the 2x nm flash devices. By tuning the incident angle of the incoming flux of Cu ions as well as utilizing the resputtering parameter, the overhang, sidewall coverage and asymmetry can be well controlled to enable complete fill by subsequent electrochemical deposition (ECD). Chemical vapor deposition (CVD) Cobalt (Co) films were also investigated as an enhancement layer for Cu gap-fill. It was observed that the insertion of a 1.5nm-thick CVD Co layer, deposited between a PVD Ta barrier and a Cu seed layer could effectively enhance gap-fill in the small geometry trench/via structures. The CVD Co enhancement layer could also significantly improve the electromigration (EM) resistance of the Cu interconnects. The Chemical Mechanical Polish (CMP) process was also developed to provide an integrated solution.
Abstract 24: Successful Control of Virtual and Robotic Hands using Neuroprosthetic Signals from Regenerative Peripheral Nerve Interfaces in a Human Subject (2018)

PURPOSE: Regenerative Peripheral Nerve Interfaces (RPNIs) show promise in controlling neuroprosthetic devices. We have implanted and recorded from RPNIs in 3 human subjects. Here, we present the results from our longest implanted subject with a distal transradial amputation. METHODS: An RPNI consists of a muscle graft that is neurotized by the distal end of a transected peripheral nerve. Once revasularized and reinnervated, the RPNI muscle graft serves as a stable bioelectric amplifier for efferent nerve action potentials and produces recordable electromyography (EMG) signals. The subject was implanted with RPNIs on the residual median, ulnar, and dorsal radial nerves. Using ultrasound, RPNIs were located, and percutaneous fine-wire bipolar electrodes were inserted for acute EMG recordings. Temporal features of the EMG waveforms (100-500Hz) were used for decoding algorithms. RESULTS: Eight months post-surgery, we recorded 300–400µV EMG signals from the median RPNI with signal-to-noise ratio (SNR) of 24.2 and 100–120µV EMG signal from the ulnar RPNI with SNR of 5.84. Additionally, EMG from residual muscles was obtained including the flexor digitorum superficialis with 100–120µV signals, SNR of 6.30, and flexor pollicis longus with ~1mV signals, SNR of 47.8. With these signals, the subject controlled a virtual robotic hand in real time with 96% accuracy, choosing 1 of 4 movements within 212 trials. Importantly, the subject controlled a physical Touch Bionics iLimb neuroprosthetic hand with 100% accuracy, choosing 1 of 3 movements within 100 trials. CONCLUSION: RPNIs harness neural signals from transected peripheral nerves with sufficient amplitude and fidelity to control an advanced neuroprosthetic limb. K.A. Carrie: None. P.P. Vu: None. Z.T. Irwin: None. P.T. Henning: None. T.A. Kung: None. C.A. Chestek: None. P.S. Cederna: None. S.W. Kemp: None.