gebhart/patrepeval huggingface dataset:
Administration of a CD25-Directed Immunotoxin, LMB-2, to Patients with Metastatic Melanoma Induces a Selective Partial Reduction in Regulatory T Cells In Vivo (2007)

CD25+ CD4+ T regulatory (Treg) cells regulate peripheral self tolerance and possess the ability to suppress antitumor responses, which may in part explain the poor clinical response of cancer patients undergoing active immunization protocols. We have previously shown that in vitro incubation of human PBMC with LMB-2, a CD25-directed immunotoxin, significantly reduced CD25+ FOXP3+ CD4+ Treg cells without impairing the function of the remaining lymphocytes. In the current study, eight patients with metastatic melanoma were treated with LMB-2 followed by MART-1 and gp100-specific peptide vaccination. LMB-2 administration resulted in a preferential, transient reduction in mean circulating CD25+ CD4+ T cell number, from 83 +/- 16 cells/microl to a nadir of 17 +/- 5 cells/microl, a 79.1% reduction. FOXP3 analysis revealed a less robust depletion with mean FOXP3+ CD4+ Treg cell number decreasing from 74 +/- 15 cells/microl to 36 +/- 8 cells/microl, a 51.4% reduction. FOXP3+ CD4+ Treg cells that survived LMB-2-mediated cytotoxicity expressed little or no CD25. Similar to the peripheral blood, immunohistochemical analysis showed a 68.9% mean reduction in FOXP3+ CD4+ Treg cell frequency in evaluable lesions. Despite inducing a reduction in Treg cell numbers in vivo, LMB-2 therapy did not augment the immune response to cancer vaccination and no patient experienced an objective response or autoimmunity. These data demonstrate the capacity of a CD25-directed immunotoxin to selectively mediate a transient partial reduction in circulating and tumor-infiltrating Treg cells in vivo, and suggest that more comprehensive Treg cell elimination may be required to bolster antitumor responses in patients with metastatic melanoma.
Novel Frequency Combs for Applications Beyond the Optics Lab (2009)

Frequency Combs are optimized for larger mode spacing by mode filtering, or with Kerr combs generated in micro toroids. New applications include precision calibration of astronomical spectrometers or the synchronisation of atomic clocks over large distances.
High-efficiency variable-speed electric motor drive technologies for energy savings in the US residential sector (2010)

Electric motors account for a substantial proportion of the electricity consumed in American homes. In order to maximize energy efficiency, the US appliance industry has increasingly adopted, over the last decade, variable speed motor technology. State of the art solutions employing high-efficiency brushless (BL) permanent magnet (PM) motors and power-electronics drives are described. These include a variety of types, such as scalar voltage-regulated BLDC and vector controlled current-regulated BLAC. The motors comprise surface PM or interior PM (IPM) rotors and 3-phase stators with distributed or concentrated windings. Single-phase low power applications are also discussed. The review covers a wide range of power between 0.002 hp and 5 hp at relatively low speeds suitable for fans and blowers and higher speeds specific to pumps and compressors. A discussion of the trends and anticipated developments is also included.
Primary Neoplasms of the Thoracic and Lumbar Spine (1990)

Primary osseous neoplasms of the thoracic and lumbar spine are uncommon lesions. Between 1965 and 1982, of 1971 patients with musculoskeletal neoplasms, only 29 (1.5%) had primary osseous tumors in these locations. There were eight children and 21 adults. Back pain was the most common complaint in 25 patients (86%), and neurologic symptoms or deficits were present in 16 patients (55%). All lesions were visible on routine spine roentgenograms, while computed tomography and myelography demonstrated spinal canal encroachment and extradural spinal cord compression in 19 patients (66%). The histologic diagnoses included 11 benign and 18 malignant lesions. Benign lesions occurred predominantly in children and malignant tumors in adults. Treatment was individualized, based on the histologic diagnoses. Twenty-two patients had surgical resection of their lesions. Laminectomy without stabilization and arthrodesis resulted in late instability and neurologic deterioration in three of seven patients (43%) with malignant lesions. Resection and decompression combined with arthrodesis did not predispose to late instability. Twenty-one patients were followed for a mean of 4.1 years (range, two to 14 years). Eight patients died from malignant disease between one month and seven years after diagnosis.
An Efficient Algorithm for Context-Aware End-to-End Connectivity Management (2009)

In a dynamic, heterogeneous environment, context-aware adaptation is a key concept to meet the varying requirements of different users. Connectivity is an important context source that can be utilized for optimal management of diverse networking resources. Application Quality of Service (QoS) is another important issue. This paper presents connectivity from the point of view of context awareness, identifies various relevant raw connectivity contexts, and discusses how high-level context information can be abstracted from the raw context information. Further, rich context information is utilized in various policy representation with respect to user profile and preference, application characteristics, device capability, and network QoS conditions. Finally, a context-aware end-to-end evaluation algorithm is presented that takes into account the application QoS .in a multi-access wireless network. Simulation results show its efficiency and effectiveness.
A periodic pattern of SNPs in the human genome (2007)

Abstract By surveying all validated SNPs in the human genome we have found that SNPs positioned 1, 2, 4, 6 or 8 bp apart are more frequent than SNPs 3, 5, 7 or 9 bp apart. This holds even when we correct for nucleotide frequencies and site dependencies in nucleotide usage in the genome. The observed pattern is not restricted to any of the genomic regions that might give sequencing or alignment errors; i.e. transposable elements (SINE, LINE and LTR), tandem repeats and large duplicated regions. However we can define periodic DNA, which virtually capture the entire pattern. Periodic DNA is defined as small DNA sequences (16.9 bp average length) with a high degree of periodicity in nucleotide usage. Periodic DNA is widely distributed in the genome, underrepresented in exons, widespread in transcripts and slightly overrepresented in tandem repeats. Furthermore periodic DNA has a 1.8 times higher SNP density than the rest of the genome.A possible biological explanation of these observations is that during DNA replication small fragments of (periodic) DNA is copied to nearby positions, substituting the original sequence. If the copied fragment differs from the original sequence a new SNP is created. In conclusion these observations suggest that not all SNPs in the human genome are created by independent single nucleotide mutations.
Suppressing quantum errors by scaling a surface code logical qubit (2023)

Practical quantum computing will require error rates well below those achievable with physical qubits. Quantum error correction<sup>1,2</sup> offers a path to algorithmically relevant error rates by encoding logical qubits within many physical qubits, for which increasing the number of physical qubits enhances protection against physical errors. However, introducing more qubits also increases the number of error sources, so the density of errors must be sufficiently low for logical performance to improve with increasing code size. Here we report the measurement of logical qubit performance scaling across several code sizes, and demonstrate that our system of superconducting qubits has sufficient performance to overcome the additional errors from increasing qubit number. We find that our distance-5 surface code logical qubit modestly outperforms an ensemble of distance-3 logical qubits on average, in terms of both logical error probability over 25 cycles and logical error per cycle ((2.914 ± 0.016)% compared to (3.028 ± 0.023)%). To investigate damaging, low-probability error sources, we run a distance-25 repetition code and observe a 1.7 × 10<sup>-6</sup> logical error per cycle floor set by a single high-energy event (1.6 × 10<sup>-7</sup> excluding this event). We accurately model our experiment, extracting error budgets that highlight the biggest challenges for future systems. These results mark an experimental demonstration in which quantum error correction begins to improve performance with increasing qubit number, illuminating the path to reaching the logical error rates required for computation.
A novel method of achieving flat spectral response arrayed waveguide grating (AWG) in silicon-on-insulator (SOI) (2003)

Arrayed Waveguide Gratings (AWG) have gained significant popularity in Wavelength Division Multiplexing (WDM) in recent years. One of the most important characteristics of an AWG is to have a flat spectral response in order to maximize the performance of the device and reduce crosstalk. In this paper, we present a novel method of achieving a flat spectral response AWG in silicon-on-insulator (SOI). This is achieved using free carrier doping, which ultimately introduces absorption which alter the intensity field distribution at the output of the array waveguides. By applying Fourier optics to the free space region of the AWG, this field profile is the inverse Fourier transform of the output field at the AWG, hence producing a flat spectral response. The rib of the arrayed waveguides is designed to operate in singlemode condition and exhibit minimum polarization dependence. The AWG is designed to operate at a centre wavelength of 1.55&mu;m at a grating order of 51 with path length differences of 22.61&mu;m. Particular emphasis is paid to the theoretical analysis and development of a flat spectral response AWG, including a number of different implantation doses.
Peroxisome Proliferator-Activated Receptor δ and γ Agonists Differentially Alter Tumor Differentiation and Progression during Mammary Carcinogenesis (2005)

Peroxisome proliferator-activated receptor (PPAR) represents a ligand-dependent nuclear receptor family that regulates multiple metabolic processes associated with fatty acid beta-oxidation, glucose utilization, and cholesterol transport. These and other receptor-mediated actions pertain to their role in hypolipidemic and antidiabetic therapies and as potential targets for cancer chemopreventive agents. The present study evaluated the chemopreventive activity of two highly potent and selective PPARgamma and PPARdelta agonists in a progestin- and carcinogen-induced mouse mammary tumorigenesis model. Animals treated with the PPARgamma agonist GW7845 exhibited a moderate delay in tumor formation. In contrast, animals treated with the PPARdelta agonist GW501516 showed accelerated tumor formation. Significantly, tumors from GW7845-treated mice were predominantly ductal adenocarcinomas, whereas tumors from GW501516-treated animals were adenosquamous and squamous cell carcinomas. Gene expression analysis of tumors arising from GW7845- and GW501516-treated mice identified expression profiles that were distinct from each other and from untreated control tumors of the same histopathology. Only tumors from mice treated with the PPARgamma agonist expressed estrogen receptor-alpha in luminal transit cells, suggesting increased ductal progenitor cell expansion. Tumors from mice treated with the PPARdelta agonist exhibited increased PPARdelta levels and activated 3-phosphoinositide-dependent protein kinase-1 (PDK1), which co-associated, suggesting a link between the known oncogenic activity of PDK1 in mammary epithelium and PPARdelta activation. These results indicate that PPARdelta and PPARgamma agonists produce diverse, yet profound effects on mammary tumorigenesis that give rise to distinctive histopathologic patterns of tumor differentiation and tumor development.
ADAPTIVE IMAGE RESTORATION USING A LOCAL NEURAL APPROACH (2007)

This work aims at defining and experimentally evaluating an iterative strategy based on neural learning for blind image restoration in the presence of blur and noise. A salient aspect of our solution is the local estimation of the restored image based on gradient descent strategies able to estimate both the blurring function and the regularized terms adaptively. Instead of explicitly defining the values of local regularization parameters through predefined functions, an adaptive learning approach is proposed. The method was evaluated experimentally using a test pattern generated by a function checkerboard in Matlab. To investigate whether the strategy can be considered an alternative to conventional restoration procedures the results were compared with those obtained by a well known neural restoration approach.
CrkL Mediates SDF-1-Induced Chemotaxis through Ras, Rac, and Erk Activation in Hematopoietic Cells. (2005)

Abstract The chemokine SDF-1 was originally identified as a growth promoting factor for pre-B cells and has been recognized to be indispensable for hematopoiesis from the findings on both its knock-out mice and those of its receptor CXCR4. SDF-1 is secreted by the bone marrow stromal cells and plays a crucial role for retention and homing of hematopoietic cells in the bone marrow through chemotaxis. In addition, SDF-1 regulates not only motility but also survival, proliferation, differentiation, and adhesion of the cells. Furthermore it was recently reported that leukemic cells show different responses to SDF-1 stimulation from normal hematopoietic cells. Despite its important roles in hematopoiesis, however, intracellular signaling pathways from CXCR4, especially those regulating chemotaxis of the hematopoietic cells, have largely remained to be clarified. We investigated the molecular mechanisms regulating chemotaxis induced by SDF-1 in hematopoietic cells and found that the enforced expression of adaptor molecule CrkL enhanced SDF-1-induced chemotaxis of murine hematopoietic cell lines, BAF3 and 32Dcl3, expressing CXCR4 on the cell surface. To examine the pathways up- and downstream of CrkL, we performed transient and stable transfection of CrkL and its mutants into BAF3 cell. Overexpression of CrkL enhanced SDF-1-induced Erk activation through Raf-1 and Mek. CrkL also enhanced SDF-1-induced activation of the Ras family GTPases Ras and Rap1 as well as the Rho family GTPase Rac. Among the dominant negative mutants of these small GTPases, those of Ras and Rac significantly suppressed CrkL-enhanced Erk activation. In addition, we also performed in vitro kinase assays using GST-CrkL as a substrate and found that SDF-1 induced phosphorylation of CrkL through the Src family tyrosine kinase Lyn. However, pretreatment with PP1, an inhibitor of Lyn, did not suppress activation of Ras, Rap1, Rac, and Erk at the concentration that suppressed the phosphorylation of CrkL. In addition, overexpression of a CrkL mutant that lacks the tyrosine targeted by Lyn did not reduce SDF-1-induced Erk activation. These results show that the phosphorylation of CrkL was not necessary for activation of the small GTPases and Erk. On the other hand, overexpression of a CrkL mutant lacking the N-terminal SH3 domain (CrkLdSH3N) required for the constitutive association with C3G, the guanine nucleotide exchange factor for Ras family GTPases, significantly reduced SDF-1-induced Erk activation. Therefore, this domain was required for the enhancement of SDF-1-induced Erk activation by CrkL through Ras. Finally we performed chemotaxis assays with transiently expressed mutants of these molecules. CrkLdSH3N as well as dominant negative forms of Ras and Rac reduced SDF-1-induced chemotaxis. Together, these results indicate that CrkL mediates SDF-1-induced chemotaxis of hematopoietic cells through activation of Ras, Rac, and the Raf/MEK/Erk pathway.
A new MOCVD platform, prismo D-Blue&#x2122;, for high-throughput GaN LED production (2013)

A new MOCVD platform, the Prismo D-Blue™, was designed and manufactured at Advanced Micro-Fabrication Equipment Inc. (AMEC) for high-volume manufacturing of high-brightness Light Emitting Diodes (LEDs). The long- term process stability and repeatability were investigated and demonstrated. Based on a well-tuned laminar gas flow condition and very stable temperature control system using dual-wavelength pyrometer sensors, more than 52 LED production runs with repeated chip performance were achieved. The LED quick test data of LED brightness, wavelength and ESD show excellent repeatability for AMEC's Prismo D-Blue™ System. In addition, various graphite susceptor designs for 4" sapphire substrates were also investigated for good wafer uniformity. With different pocket depth for inner-ring and outer-ring, good susceptor (14×4" LED wafers) wavelength uniformity of <;1.6 nm was achieved.
Non-invasive evaluation of therapeutic response in keloid scar using diffuse reflectance spectroscopy (2015)

The pathogenesis and ideal treatment of keloid are still largely unknown, and it is essential to develop an objective assessment of keloid severity to evaluate the therapeutic response. We previously reported that our diffuse reflectance spectroscopy (DRS) system could assist clinicians in understanding the functional and structural condition of keloid scars. The purpose of this study was to understand clinical applicability of our DRS system on evaluating the scar severity and therapeutic response of keloid. We analyzed 228 spectral data from 71 subjects with keloid scars. The scars were classified into mild (0-3), moderate (4-7) and severe (8-11) according to the Vancouver scar scale. We found that as the severity of the scar increased, collagen concentration and water content increased, and the reduced scattering coefficient at 800 nm and oxygen saturation (SaO2) decreased. Using the DRS system, we found that collagen bundles aligned in a specific direction in keloid scars, but not in normal scars. Water content and SaO2 may be utilized as reliable parameters for evaluating the therapeutic response of keloid. In conclusion, the results obtained here suggest that the DRS has potential as an objective technique with which to evaluate keloid scar severity. In addition, it may be useful as a tool with which to track longitudinal response of scars in response to various therapeutic interventions.
Engrailed homeoproteins in visual system development (2014)

Engrailed is a homeoprotein transcription factor. This family of transcription factors is characterized by their DNA-binding homeodomain and some members, including Engrailed, can transfer between cells and regulate protein translation in addition to gene transcription. Engrailed is intimately involved in the development of the vertebrate visual system. Early expression of Engrailed in dorsal mesencephalon contributes to the development and organization of a visual structure, the optic tectum/superior colliculus. This structure is an important target for retinal ganglion cell axons that carry visual information from the retina. Engrailed regulates the expression of Ephrin axon guidance cues in the tectum/superior colliculus. More recently it has been reported that Engrailed itself acts as an axon guidance cue in synergy with the Ephrin system and is proposed to enhance retinal topographic precision.
ChemInform Abstract: SUBSTITUENT EFFECTS IN THE CONTROL OF THE OXIDATION‐REDUCTION PROPERTIES OF METAL IONS IN COMPLEXES WITH MACROCYCLIC LIGANDS (1981)

Abstract Makrocyclische Methyl‐Acetyl‐substituierte Ni‐Komplexe (I) mit 14, 15 und 16 Ringgliedern sind aus Diketonen durch Umsetzung mit Acetanhydrid in Gegenwart von Triethylorthoformiat, Zugabe von Diaminen NH, ‐X‐NH2, Reaktion mit Ni‐acetat und Zugabe von Diaminen NH,‐ Y‐NH, nach beschriebener Methode zugänglich.
Predicting the Activity of Single Isolated Lewis Acid Sites in Solid Catalysts (2006)

An experimental study of the activity of Ti-, Zr- and Sn-beta catalysts in different types of oxidation reactions is combined with a quantum-chemical analysis of the electronic properties of the active sites and the adsorbed reactants. The differences observed in the catalytic behaviour of the three materials are explained in terms of the molecular orbital distribution of each system. The intrinsic Lewis acid strength of the isolated active site, the degree of back-donation from the catalyst to the empty orbitals of the organic reactant and the net atomic charges on selected atoms are proposed as predictors of reactivity.
Intestinal epithelial spheroids: new tools for studying gastrointestinal diseases (2014)

The intestinal tract is one of the most complex organs of our body because it has to perform several functions, including digestion and absorption of nutrients. Being exposed to a continuous insult by the local microbiota, the intestinal epithelium is constantly renewed from Lgr5+ stem cell progenitors located in the crypts of Lieberkuhn.1 These progenitors have been recently exploited to regenerate ‘mini-guts’ (organoids) in vitro.2 An appropriate cocktail of small molecules and growth factors has been identified that preserves stemness but also favours the differentiation of enterocytes and Paneth cells thus forming the organotypic structure of a crypt-villous organoid (for a review, see ref. 3).

In this issue of Gut , VanDussen et al 4 show a powerful method of growing human epithelial cells in culture from biopsies of several intestinal segments of either healthy individuals or patients with several pathologies. 

The authors established a very simple methodology starting from biopsies collected during routine endoscopy. Crypts were isolated with collagenase digestion and embedded in matrigel with 50% conditioned medium obtained from fibroblasts engineered to secrete Wnt3a, R-spondin and Noggin.5 These three factors were previously shown by the same authors among others to be sufficient to propagate and maintain intestinal epithelial cells in the mouse system.3 

In the current manuscript, …
Liquid source metal–organic chemical-vapor deposition of high-quality YBa2Cu3O7−x films on polycrystalline silver substrates (1998)

High-temperature superconducting YBa2Cu3O7−x films were grown by liquid delivery metal–organic chemical-vapor deposition on silver-coated stainless-steel substrates. The films are highly c-axis oriented, have a Tc above 90 K, and exhibit a surface resistance of 110 μΩ at 77 K and 3 GHz.
The Role of Protein Kinase A in Anxiety Behaviors (2016)

This review focuses on the genetic and other evidence supporting the notion that the cyclic AMP (cAMP) signaling pathway and its mediator, the protein kinase A (PKA) enzyme, which respond to environmental stressors and regulate stress responses, are central to the pathogenesis of disorders related to anxiety. We describe the PKA pathway and review in vitro animal studies (mouse) and other evidence that support the importance of PKA in regulating behaviors that lead to anxiety. Since cAMP signaling and PKA have been pharmacologically exploited since the 1940s (even before the identification of cAMP as a second messenger with PKA as its mediator) for a number of disorders from asthma to cardiovascular diseases, there is ample opportunity to develop therapies using this new knowledge about cAMP, PKA, and anxiety disorders.
Low-speed position sensorless drive for highly efficient permanent magnet synchronous motor without rare-earth metals (2013)

In this paper, we discuss a position sensorless drive for an axial structure motor without rare-earth metals in a low-speed region. Since this motor has no saliency, a conventional position sensorless drive using harmonic injection cannot be applied. Therefore, we apply a position sensorless drive based on Induced Voltage caused by Magnetic Saturation (IVMS) to this motor. As IVMS becomes very small for motors without saliency, we introduce a differential amplifier and adjust its gain appropriately. We implemented this method by using a microcomputer and an analog circuit. As a result, excellent drive performance in a low-speed region was obtained in experiments for the motor (200V/11kW).