gebhart/patrepeval huggingface dataset:
Gene expression based risk classification in multiple myeloma (2018)

This thesis focuses on gene expression profiling (GEP) to identify multiple myeloma (MM) patients with high-risk disease. \n\nToday primarily patient specific factors such as age, the presence of comorbidities, frailty and renal failure are used for treatment decisions. As a result, almost all newly diagnosed MM patients receive similar treatment. This treatment has been shown to be effective in the MM patient group as a whole. However, some patients respond only minimally or do not respond at all requiring treatment adjustments. This approach therefore fails to produce the best response in each patient. \n\nIn the future molecular biomarkers are likely to guide treatment decisions by identifying treatment specific markers for both toxicities and response. In the absence of reliable predictions, treatments can be adapted based on risk stratification. In this way, a most optimal treatment for each patient can be selected in order to achieve a better quality of life, deeper responses and possibly even a cure. \n\nAs a primary result we have shown that the EMC92-gene classifier is a valid prognostic marker. It effectively identifies a high-risk group of 18% of patients with unfavorable median survival of 24 months, independent of other prognostic markers. In combination with ISS, the EMC92 marker was able to identify 38% of patients with a favorable median survival which was not reached after 96 months. This thesis also highlights the power of routinely applied markers such as cytogenetics and ISS. Risk adapted strategies, hopefully coupled to predictive markers, must determine the best way to improve survival of this as yet incurable disease.
BEK, a receptor for multiple members of the fibroblast growth factor (FGF) family, maps to human chromosome 10q25.3→q26 (1992)

The gene for the fibroblast growth factor receptor BEK was assigned to human chromosome 10 by applying polymerase chain reaction techniques to DNAs from a panel of human x rodent somatic cell hybrids. The gene was further localized to 10q25.3----q26 by in situ hybridization.
Analysis of fast sparse superposition codes (2011)

Sparse superposition codes with a fast adaptive successive decoder for the additive white Gaussian noise channel were introduced last year by the authors, along with presentation of reliability at rates approaching capacity. The present work presents ingredients of the distributional analysis of the decoder.
Energy-Efficient Cooperative Relaying over Fading Channels with Simple Relay Selection (2008)

We consider a cooperative wireless network where a set of nodes cooperate to relay in parallel the information from a source to a destination using a decode-and-forward approach. The source broadcasts the data to the relays, some or all of which cooperatively beamform to forward the data to the destination. We generalize the standard approaches for cooperative communications in two key respects: (i) we explicitly model and factor in the cost of acquiring channel state information (CSI), and (ii) we consider more general selection rules for the relays and compute the optimal one among them. In particular, we consider simple relay selection and outage criteria that exploit the inherent diversity of relay networks and satisfy a mandated outage constraint. These criteria include as special cases several relay selection criteria proposed in the literature. We obtain expressions for the total energy consumption for general relay selection and outage criteria for the non-homogeneous case, in which different relay links have different mean channel power gains, and the homogeneous case, in which the relay links statistics are identical. We characterize the structure of the optimal transmission scheme. Numerical results show that the cost of training and feedback of CSI is significant. The optimal strategy is to use a varying subset (and number) of relay nodes to cooperatively beamform at any given time. Depending on the relative location of the relays, the source, and the destination, numerical computations show energy savings of about 16% when an optimal relay selection rule is used. We also study the impact of shadowing correlation on the energy consumption for a cooperative relay network.
Circularly Polarized Spidron Fractal Dielectric Resonator Antenna (2015)

In this letter, a circularly polarized Spidron fractal dielectric resonator antenna is presented. A wide 3-dB axial ratio (AR) bandwidth is realized by merging a Spidron fractal dielectric resonator and a C-shaped slot that can produce circular polarization. The proposed antenna is excited through the coupling between a C-shaped slot in the ground plane and a 50-Ω microstrip feeding line. A prototype of the antenna is fabricated and tested. Reasonable agreement is achieved between the measurement and simulation. The experimental results show that the proposed antenna has a -10- dB reflection bandwidth of 37.29% (4.32-6.30 GHz) and a 3-dB AR bandwidth of 11.57% (5.13-5.76 GHz). The measured gain of the antenna ranges 2.20 dBic to 3.16 dBic within the AR bandwidth.
A Compression scheme for archiving DNA sequencing images (2008)

DNA sequencing today produces vast amounts of image data in the final recording process. For example, Solexapsilas sequencing by synthesis platform allows the outcome of sequencing reactions to be observed simultaneously at a resolution of millions of individual DNA molecules. Recording the outcome after each reaction therefore, generates terabytes of image data in the course experimentation. For posterity reasons some of this image data needs to be preserved for longer term and therefore we need compression schemes with high compression ratios while data fidelity needs to be preserved. This paper describes the design and implementation of a novel compression scheme for archiving DNA Sequencing Images produced during the sequencing by synthesis procedure. The scheme is based on the identification of information points in the sequencing images, and regeneration of the whole image using these, exploiting diffraction characteristics of point sources of light. It provides for a high compression ratio of 1:10 to 1:20, while still maintaining acceptable fidelity of the information.
High-power, high-brightness continuous-wave interband cascade lasers with tapered ridges (2013)

We report tapered-ridge mid-infrared (λ = 3.75 μm) interband cascade lasers emitting up to 403 mW of continuous wave output power at T = 25 °C, with beam quality characterized by M2 = 2.3. One index-guided tapered structure consisted of a single 4-mm-long section with ridge width varying linearly from 5 μm to 63 μm. Another device that combined a narrow ridge of uniform width with a tapered section produced slightly lower maximum output power and brightness.
Electromagnetic redesign of the HYPERcollar applicator: toward improved deep local head-and-neck hyperthermia (2013)

Accumulating evidence shows that hyperthermia improves head-and-neck cancer treatment. Over the last decade, we introduced a radiofrequency applicator, named HYPERcollar, which enables local heating also of deep locations in this region. Based on clinical experience, we redesigned the HYPERcollar for improved comfort, reproducibility and operator handling. In the current study, we analyze the redesign from an electromagnetic point of view. We show that a higher number of antennas and their repositioning allow for a substantially improved treatment quality. Combined with the much better reproducibility of the water bolus, this will substantially minimize the risk of underexposure. All improvements combined enable a reduction of hot-spot prominence (hot-spot to target SAR quotient) by 32% at an average of 981 W, which drastically reduces the probability for system power to become a treatment limiting source. Moreover, the power deposited in the target selectively can be increased by more than twofold. Hence, we expect that the HYPERcollar redesign currently under construction allows us to double the clinically applied power to the target while reducing the hot-spots, resulting in higher temperatures and, consequently, better clinical outcome.
Aislamiento y caracterización de un nuevo fago filamentoso de Vibrio cholerae capaz de transducir los genes de la toxina colérica. (2007)

Un nuevo bacteriófago filamentoso, designado VEJ¿, se aisló de la cepa de Vibrio cholerae MO45 del serogrupo O139. Se realizó una caracterización molecular preliminar de este fago, que incluyó la secuenciación de su genoma completo, el estudio de la estructura genómica y la identificación del receptor del fago, así como del gen que codifica la proteína mayoritaria de la cápsida mediante la secuenciación de la región amino terminal de esta última. La secuencia nucleotídica del genoma de VEJ¿, de 6842 bp, reveló que presenta una organización modular de genes funcionalmente relacionados, que es característica del género de los inovirus (fagos filamentosos). VEJ¿ está estrechamente relacionado con otros fagos filamentosos de Vibrio cholerae descritos previamente, entre los que se incluyen VGJ¿, VSK y fs1. Al igual que estos\núltimos, VEJ¿ utiliza como receptor celular a la fimbria de tipo IV denominada hemaglutinina sensible a manosa (MSHA). Se demostró que VEJ¿, al igual que el fago VGJ¿, es capaz de transmitir horizontalmente el genoma del fago CTX¿ y por tanto, los genes de la toxina colérica entre poblaciones bacterianas de Vibrio cholerae que expresan la fimbria MSHA. Los resultados del presente trabajo sugieren que la variedad de fagos implicados en los eventos de transmisión horizontal de los genes de la toxina colérica puede ser mayor de lo que se pensaba.
Multispectral image enhancement by spectral shifting (2012)

A multispectral enhancement method that preserves the natural color of the background pixels was previously proposed. In such method, the band for enhancement was identified from the N-band spectral residual-error of the objects of interest. The spectral residual-error is determined by taking the difference between the original spectrum of the pixel and its estimate using M<<N principal components in principal component analysis (PCA). However, for stained histopathology images where staining variations do exist even among tissue sections the band for enhancement could vary. In this work, we introduced a modification to the previously proposed multispectral enhancement method such that the band for enhancement could be specified independent of the spectral residualerror configurations. In the proposed modification the original spectral transmittance of the pixels at each band are shifted by the product between the spectral residual-error coefficient, which is the most dominant PC coefficient of the spectral error, of the pixel and the weighting factor assigned by the user to each band. Results of our experiments on H&E stained sections of liver tissue show that the proposed modification delivers more consistent enhancement results compared to the previously proposed methods, especially when the band for enhancement varies.
Nanoporous Alumina Template with In Situ Barrier Oxide Removal, Synthesized from a Multilayer Thin Film Precursor (2005)

A nanoporous alumina template made from a multilayer metal film structure has been developed that allows for the in situ removal of the electrically insulating alumina barrier layer, exposing a Pt electrode at the pore bases. This barrier-free nanoporous system is of great use for dc electrodeposition of a wide variety of materials in the alumina pores. This work in particular describes the development of a multilayer thin film precursor consisting of a Si substrate with thin Pt and Ti and a thicker Al layer in that order. After the Al is anodized, producing the porous alumina, the resulting is selectively removed at the base of the alumina pores exposing the Pt electrode. The metals in the precursor perform different roles in the fabrication and allow the alumina template to be fabricated directly on the final substrate with no film transfer technique involved. This allows Si to be used as the substrate, which could then include electronic circuitry. Several techniques are used to analyze the resulting template.
Isolation of novolak resin at low temperature (1996)

It is a well known fact that novolak resin undergoes chemical structure changes using vigorous synthesis conditions, such as under high acid catalyst loading and high temperature during isolation. Under such conditions, the structure of novolak resin is rearranged through quinone methide intermediate. We have also observed that the rearranged novolak resin does not perform well in photolithography. In this paper we discus the alternate isolation procedure, eliminating high temperature vacuum distillation. In this process a typical resin synthesis is performed using cresylic acids, catalyst and a solvent with the addition of formaldehyde over time. At the end of the condensation period, distillation is applied using a sub-surface high forced steam. Distillation is performed until all the unreacted cresols are removed. At this point the temperature is raised up to 140 degrees Celsius, and the vacuum is slowly drawn to 35 mm Hg to remove residual water. After the volatiles have been distilled off, the vacuum is released and a solvent is added to adjust the solid content. We discuss in this paper, the properties of the resin in the application of photolithography.
Abstract 486: Allogeneic Mesenchymal Stem Cells in Cellular Cardiomyoplasty: Mechanisms of Cardiac Repair (2008)

Background- Although there is significant enthusiasm for cell-based therapies, whether administered cells differentiate into cardiomyocytes (CM) or exert their effects solely by paracrine signaling remains controversial. We hypothesized that allogeneic bone marrow-derived mesenchymal stem cells (aMSCs) regenerate the infarcted heart by cell autonomous mechanisms involving differentiation into myocytes, endothelial cells, vascular smooth muscle cells and the stimulation of endogenous precursor cell proliferation. Methods and Results - Seventeen female swine underwent myocardial infarction. Three days later, they received intramyocardial injections of male GFP pos aMSCs (n=7), placebo (n=7) or no injection (n=3). Animals were euthanized at 24h (n=1 aMSCs, n=1 placebo), 72h (n=3 aMSCs, n=3 placebo) and 2 weeks (n=3 aMSCs, n=3 placebo, n=3 controls) after injections. Within 24h, engrafted aMSCs exhibited lineage commitment into CM (GATA4, α-sarcomeric actinin) but not vascular precursors. By 72h, CM differentiation rates increased substantially (GFP pos /GATA pos : 23.4±3.2% of GFP pos cells at 72h vs 13.4±5.4% at 24h) as well as vascular lineage committment (GFP pos /KDR/Factor VIII pos : 1.3±0.4%). Importantly, aMSCs migrated throughout ischemic but not viable myocardium. Two weeks later, MSCs had differentiated into mature vessels and CM. Cardiac regeneration was accompanied by recruitment of endogenous c-kit pos cells at infarct (IZ) and border (BZ) zones of the treated animals, compared both to placebo and control (p≤0.001). In contrast to the untreated animals, c-kit cells were localized in clusters in the IZ and BZ of the treated hearts and formed connexin-43 and N-cadherin connections with each other and the GFP pos aMSCs, resembling stem cell niches. The number of the c-kit pos /GATA-4 pos cells within the niches was significantly higher at the BZ of the treated hearts (3.9±1.6%) compared to placebo and control (p≤0.05), indicative of an endogenous repair mechanism. Conclusions- Together these findings offer important mechanistic insight into the basis of aMSCs ability to achieve post-MI cardiac regeneration, and illustrate that the cells exert both cell dependent and host dependent effects.
New Synthetic Technology for Efficient Construction of α-Hydroxy-β-amino Amides via the Passerini Reaction<sup>1</sup> (2000)

[reaction: see text] The Passerini reaction of N-protected amino aldehydes, isonitriles, and TFA using pyridine-type bases proceeds under mild conditions and directly affords alpha-hydroxy-beta-amino amide derivatives in moderate to high yields. These adducts are readily hydrolyzed to alpha-hydroxy-beta-amino carboxylic acids. Application of these key intermediates to concise syntheses of P(1)-alpha-ketoamide protease inhibitors is illustrated.
Expression and action of cyclic GMP-dependent protein kinase Iα in inflammatory hyperalgesia in rat spinal cord (1999)

Several lines of evidence have shown a role for the nitric oxide/cyclic guanosine monophosphate signaling pathway in the development of spinal hyperalgesia. However, the roles of effectors for cyclic guanosine monophosphate are not fully understood in the processing of pain in the spinal cord. The present study showed that cyclic guanosine monophosphate-dependent protein kinase Ialpha but not Ibeta was localized in the neuronal bodies and processes, and was distributed primarily in the superficial laminae of the spinal cord. Intrathecal administration of a selective inhibitor of cyclic guanosine monophosphate-dependent protein kinase Ialpha, Rp-8-[(4-chlorophenyl)thio]-cGMPS triethylamine, produced a significant antinociception demonstrated by the decrease in the number of flinches and shakes in the formalin test. This was accompanied by a marked reduction in formalin-induced c-fos expression in the spinal dorsal horn. Moreover, cyclic guanosine monophosphate-dependent protein kinase Ialpha protein expression was dramatically increased in the lumbar spinal cord 96 h after injection of formalin into a hindpaw, which occurred mainly in the superficial laminae on the ipsilateral side of a formalin-injected hindpaw. This up-regulation of cyclic guanosine monophosphate-dependent protein kinase Ialpha expression was completely blocked not only by a neuronal nitric oxide synthase inhibitor, 7-nitroindazole, and a soluble guanylate cyclase inhibitor, 1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one, but also by an N-methyl-D-aspartate receptor antagonist, dizocilpine maleate (MK-801). The present results indicate that noxious stimulation not only initially activates but also later up-regulates cyclic guanosine monophosphate-dependent protein kinase Ialpha expression in the superficial laminae via an N-methyl-D-aspartate-nitric oxide-cyclic guanosine monophosphate signaling pathway, suggesting that cyclic guanosine monophosphate-dependent protein kinase Ialpha may play an important role in the central mechanism of formalin-induced inflammatory hyperalgesia in the spinal cord.
Optimal PET Protection for Streaming Scalably Compressed Video Streams With Limited Retransmission Based on Incomplete Feedback (2010)

For streaming scalably compressed video streams over unreliable networks, Limited-Retransmission Priority Encoding Transmission (LR-PET) outperforms PET remarkably since the opportunity to retransmit is fully exploited by hypothesizing the possible future retransmission behavior before the retransmission really occurs. For the retransmission to be efficient in such a scheme, it is critical to get adequate acknowledgment from a previous transmission before deciding what data to retransmit. However, in many scenarios, the presence of a stochastic packet delay process results in frequent late acknowledgements, while imperfect feedback channels can impair the server's knowledge of what the client has received. This paper proposes an extended LR-PET scheme, which optimizes PET-protection of transmitted bitstreams, recognizing that the received feedback information is likely to be incomplete. Similar to the original LR-PET, the behavior of future retransmissions is hypothesized in the optimization objective of each transmission opportunity. As the key contribution, we develop a method to efficiently derive the effective recovery probability versus redundancy rate characteristic for the extended LR-PET communication process. This significantly simplifies the ultimate protection assignment procedure. This paper also demonstrates the advantage of the proposed strategy over several alternative strategies.
Phonologically-based biomarkers for major depressive disorder (2011)

Abstract Of increasing importance in the civilian and military population is the recognition of major depressive disorder at its earliest stages and intervention before the onset of severe symptoms. Toward the goal of more effective monitoring of depression severity, we introduce vocal biomarkers that are derived automatically from phonologically-based measures of speech rate. To assess our measures, we use a 35-speaker free-response speech database of subjects treated for depression over a 6-week duration. We find that dissecting average measures of speech rate into phone-specific characteristics and, in particular, combined phone-duration measures uncovers stronger relationships between speech rate and depression severity than global measures previously reported for a speech-rate biomarker. Results of this study are supported by correlation of our measures with depression severity and classification of depression state with these vocal measures. Our approach provides a general framework for analyzing individual symptom categories through phonological units, and supports the premise that speaking rate can be an indicator of psychomotor retardation severity.
A Nuclear Inhibitor of NF-κB Encoded by a Poxvirus (2010)

Poxviruses have evolved various strategies to inhibit cytoplasmic events leading to activation of the nuclear factor κB (NF-κB) signaling pathway, with individual viruses often encoding multiple NF-κB inhibitors. Here, the novel orf virus (ORFV)-encoded protein ORFV002 was shown to inhibit nuclear events regulating NF-κB transcriptional activity. ORFV002 expression in cell cultures significantly decreased wild-type-virus-, tumor necrosis factor alpha (TNF-α)-, and lipopolysaccharide (LPS)-induced NF-κB-mediated gene expression. Expression of ORFV002 in cells, while not affecting phosphorylation or nuclear translocation of NF-κB-p65, markedly decreased TNF-α- and wild-type-virus-induced acetylation of NF-κB-p65, a p300-mediated nuclear modification of NF-κB-p65 that regulates its transactivating activity. ORFV002 was shown to colocalize and interact with NF-κB-p65, and expression of ORFV002 in cell cultures resulted in a reduced interaction of NF-κB-p65 with p300, suggesting that ORFV002 interferes with NF-κB-p65/p300 association. Deletion of ORFV002 from the OV-IA82 genome had no significant effect on ORFV pathogenesis in sheep, indicating that ORFV002 is nonessential for virus virulence in the natural host. This represents the first description of a nuclear inhibitor of NF-κB encoded by a poxvirus.
An Automata-Theoretic Approach for Model Checking Threads for LTL Propert (2006)

In this paper, we propose a new technique for the verification of concurrent multi-threaded programs. In general, the problem is known to be undecidable even for programs with just two threads. However, we exploit the observation that, in practice, a large fraction of concurrent programs can either be modeled as pushdown systems communicating solely using locks or can be reduced to such systems by applying standard abstract interpretation techniques or by exploiting separation of data from control. Moreover, standard programming practice guidelines typically recommend that programs use locks in a nested fashion. In fact, in languages like Java and C#, locks are guaranteed to be nested. For such a framework, we show, by using the new concept of Lock Constrained Multi-Automata Pair (LMAP), that pre*-closures of regular sets of states can be computed efficiently. This is accomplished by reducing the pre*-closure computation for a regular set of states of a concurrent program with nested locks to those for its individual threads. Leveraging this new technique then allows us to formulate a fully automatic, efficient and exact (sound and complete) decision procedure for model checking threads communicating via nested locks for indexed linear-time temporal logic formulae