gebhart/patrepeval huggingface dataset:
Prediction of Relapse By microRNA Expression in Pediatric B-Lineage Acute Lymphoblastic Leukemia (2014)

Abstract Aim: microRNAs (miRs) have been implicated in many malignancies. Our aim was to identify specific miRNAs that can predict risk of relapse in pediatric acute lymphoblastic leukemia (ALL) patients treated on BFM protocols, better than the current risk group stratification. Currently, the main method for risk group stratification is based on the amount of minimal residual disease (MRD) assessed at specific time points by real time quantitative PCR (RQ-PCR). Material and methods: Following microRNA expression analysis performed on 48 bone marrow samples at diagnosis, we focused on several miRs that correlated with at least 3 of the established prognostic markers in ALL to be validated in a cohort of 138 B-lineage ALL samples. Of the miRs studied, down regulated miR-151-5p and miR-451 and upregulated miR-1290 significantly correlated with outcome. Results: Low expression of miR-151-5p, miR-451 or of both together resulted in significantly worse relapse free survival (RFS) (56%, 63% and 47%, respectively) compared to RFS rates when either or both miRs were highly expressed (80%, 78% and 78%, respectively) (p=0.007, 0.042 and 0.002, respectively). High expression of miR-1290 resulted in worse RFS compared to those that expressed low levels (54% versus 81%; p=0.014). When combining the 3 miRs, a patient expressing low levels of both miRs and/or high levels of miR-1290 had a RFS of 54% (p=0.004). Furthermore, the expression of the 3 miRs could distinguish within the TEL-AML1 negative cohort two groups; one with 80% and the other with 44% RFS (p=0.004). Multivariate Cox regression analysis identified low expression of both miRs and/or high expression of miR-1290 as an independent prognostic marker in the PCR-MRD non-high risk cohort. Patients expressing abnormal levels of the 3 miRs had a 4.47-fold increased risk for relapse (p=0.037). Deletion of IKZF1 gene is a known adverse prognostic marker in B-lineage ALL. In 85 patients, IKZF1 status was analyzed and 9 patients were found to harbor the deletion. The expression of the 3 miRs could still identify an adverse group of patients with 69% RFS within the group with no deletion (p=0.004). When adding IKZF1 and TEL-AML1 status to the Multivariate analysis in addition to PCR-MRD, the expression of the 3 miRs remained a significant independent marker with a 24 fold increased risk for relapse (p=0.011). Figure 1 Figure 1. Conclusion: Our results identify the combination of miR-151-5p, miR-451 and miR-1290 as a novel biomarker for outcome in pediatric B-lineage ALL patients, already at time of diagnosis. This may lead to improved risk group stratification and enable early therapeutic intervention that may result in better RFS. Disclosures No relevant conflicts of interest to declare.
Reversible Complexation Mediated Polymerization (RCMP) of Methyl Methacrylate (2012)

A new family of living radical polymerization using amines as organic catalysts was introduced. It was based on a new reversible activation mechanism, reversible complexation. The polymer molecular weight (M n being up to 30,000) and its distribution (M w/M n = 1.2–1.4) were well controlled in the polymerizations of methyl methacrylate. The catalysts included such common amines as triethylamine. Their low cost, good environmental safety, and ease of handling may be attractive for possible applications. The method using the alkyl iodide (low-mass dormant species) in situ generated in the polymerization was also successfully adopted to this polymerization.
Body-acoustic device (1997)

A body-acoustic device is provided which comprises a housing (1), a diaphragm (4) dividing an inner space of the housing into a first chamber (5) and a second chamber (6), and a loudspeaker (7) mounted to an opening provided in the diaphragm, wherein the diaphragm is made of a transversely vibratory member and/or has a perimetric edge supported by an inner surface of the housing via an elastic member (10), and wherein the diaphragm (4) is further provided with a port (9) for air movement between the first and second chambers (5), (6). When the loudspeaker (7) is operated, the diaphragm vibrates with a cone paper (8) to generate sufficient heavy bass sound with high sound clarity as if the diameter of the loudspeaker had increased. The port provided in the vibrating diaphragm facilitates the vibration of the diaphragm, further increasesing the sound pressure created by the diaphragm vibration due a sound throttling effect caused by the port. As a result, sufficient and clear body-felt sound, especially heavy bass sound, can be obtained through vibration of the housing outer walls.
Spectropolarimetric imaging using a field-portable imager (2000)

The Army Research Laboratory has a program to develop and characterize compact field-portable hyperspectral and polarization imagers using electronically tunable spectral filters—acousto-optic tunable filters (AOTFs)—that are polarization sensitive. A spectropolarimetric imager has been designed that combines a liquid-crystal retardation plate with an AOTF and an off-the-shelf charge coupled device (CCD) camera. The imager uses a tellurium dioxide (TeO2) AOTF that operates from the visible to the near-infrared region. The imager is relatively compact, lightweight, and programmable. We used this imager to collect spectral and polarization data from various objects and backgrounds, both in the laboratory and in field tests. The spectral images were collected from 450 to 1000 nm at 10- or 20-nm intervals, at two or four polarization settings for each spectral interval. We analyzed a portion of these data to assess the effectiveness of this system for target detection and identification. Here we present and discuss our measurements and analysis results.
A structured approach to post-silicon validation and debug using symbolic quick error detection (2015)

During post-silicon validation and debug, manufactured integrated circuits (ICs) are tested in actual system environments to detect and fix design flaws (bugs). Existing post-silicon validation and debug techniques are mostly ad hoc and often involve manual steps. Such ad hoc approaches cannot scale with increasing IC complexity. We present Symbolic Quick Error Detection (Symbolic QED), a structured approach to post-silicon validation and debug. Symbolic QED combines the following steps in a coordinated fashion: 1. Quick Error Detection (QED) tests that quickly detect bugs with short error detection latencies and high coverage. 2. Formal analysis techniques to localize bugs and generate minimal-length bug traces upon detection of the corresponding bugs. We demonstrate the practicality and effectiveness of Symbolic QED using the OpenSPARC T2, a 500-million-transistor open-source multicore System-on-Chip (SoC) design, and using "difficult" logic bug scenarios that occurred in various state-of-the-art commercial multicore SoCs. Our results show that Symbolic QED: (i) is fully automatic (unlike manual techniques in use today that can be extremely time-consuming and expensive); (ii) requires only a few hours in contrast to manual approaches that might take days (or even months) or formal techniques that often take days or fail completely for large designs; (iii) generates counter-examples (for activating and detecting logic bugs) that are up to 6 orders of magnitude shorter than those produced by traditional techniques; and, (iv) does not require any additional hardware.
Channel Geometry Impact and Narrow Sheet Effect of Stacked Nanosheet (2018)

The characteristics of Stacked Nanosheet are investigated, focusing on channel geometry. For the first time, “narrow sheet effect” on carrier transport is observed. By comparing measured electron <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$(\mu_{e})$</tex> and hole <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$(\mu_{h})$</tex> mobilities, and the n-type/p-type opposite transconductance ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$gm$</tex> ) trends versus sheet width ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$Wsheet$</tex> ), we show that the mobility dependency on <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$Wsheet$</tex> is attributed to reduced (100) plane conduction contribution as <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$Wsheet$</tex> shrinks.
A non-intrusive signal-based model for speech quality evaluation using automatic classification of background noises (2009)

This paper describes an original method for speech quality evaluation in the presence of different types of background noises for a range of communications (mobile, VoIP, RTC). The model is obtained from subjective experiments described in [1]. These experiments show that background noise can be more or less tolerated by listeners, depending on the sources of noise that can be identified. Using a classification method, the background noises can be classified into four groups. For each one of the four groups, a relation between loudness of the noise and speech quality is proposed.
Noise and the detection of coronary artery disease with an electronic stethoscope (2010)

Recent studies demonstrated that diastolic heart sounds, recorded with an electronic stethoscope, contain markers of coronary artery disease (CAD). A difficult is that the CAD-related sound is very weak and recordings are often contaminated by noise. The current study analyses the noise contamination of 633 stethoscope recordings from a clinical environment. Respiration noise, ambient noise, recording noise and abdominal noise were identified in the recordings and were classified according to duration and intensity. To monitor how noise influences the classification performance AR-pole magnitudes were extracted from both the 25-250 Hz frequency band and the 250-1000 Hz frequency band. The classification performance was quantified by the Area Under the receiver operating Characteristic (AUC). Ambient noise was present in 39.9% of the recordings and was the most common noise source. Abdominal noise was the least common noise source, present in 10.8% of the recordings. The best pole, with respect to detection of CAD, extracted from the 250-1000 Hz frequency band was sensitive to noise, since the AUC dropped from 0.70 in to 0.57 when noisy recordings were included. Contrary the best pole from the 25-250 Hz frequency band was relatively robust against noise, since the AUC dropped from 0.73 to only 0.70 when noisy recordings were included. The study demonstrated that noise contamination is a frequent problem and that features from lower frequency bands are more robust against noise than features from higher frequency bands.
A digitally controlled integrated DC-DC converter with transient suppression (2010)

A fully integrated DC-DC converter with digitally controlled dual output stages is introduced in this paper. An auxiliary output stage is added in parallel to the main output switching stage to mitigate the trade-off between fast load transient response and high power conversion efficiency. A 12V-to-1V, 3W voltage-control-mode prototype converter is designed and fabricated with TSMC 0.25µm 40V process. Experimental result shows that this method can reduce the transient overshoot by 50% and recovery time by 80% while maintaining similar efficiency when comparing to a conventional single-stage converter. The auxiliary stage imposed less than 20% area overhead.
Scaling waveguide-integrated superconducting nanowire single-photon detector solutions to large numbers of independent optical channels (2022)

Superconducting nanowire single-photon detectors are an enabling technology for modern quantum information science and are gaining attractiveness for the most demanding photon counting tasks in other fields. Embedding such detectors in photonic integrated circuits enables additional counting capabilities through nanophotonic functionalization. Here we show how a scalable number of waveguide-integrated superconducting nanowire single-photon detectors can be interfaced with independent fiber optic channels on the same chip. Our plug-and-play detector package is hosted inside a compact and portable closed-cycle cryostat providing cryogenic signal amplification for up to 64 channels. We demonstrate state-of-the-art photon counting performance with up to 60 % system detection efficiency and down to 26.0 ps timing accuracy for individually addressable detectors. Our multi-channel single photon receiver offers exciting measurement capabilities for future quantum communication, remote sensing and imaging applications.
Human Breast Cancer: Correlation of Relapse and Survival with Amplification of the HER-2/<i>neu</i>Oncogene (1987)

The HER-2/neu oncogene is a member of the erbB-like oncogene family, and is related to, but distinct from, the epidermal growth factor receptor. This gene has been shown to be amplified in human breast cancer cell lines. In the current study, alterations of the gene in 189 primary human breast cancers were investigated. HER-2/neu was found to be amplified from 2- to greater than 20-fold in 30% of the tumors. Correlation of gene amplification with several disease parameters was evaluated. Amplification of the HER-2/neu gene was a significant predictor of both overall survival and time to relapse in patients with breast cancer. It retained its significance even when adjustments were made for other known prognostic factors. Moreover, HER-2/neu amplification had greater prognostic value than most currently used prognostic factors, including hormonal-receptor status, in lymph node-positive disease. These data indicate that this gene may play a role in the biologic behavior and/or pathogenesis of human breast cancer.
Tailoring the Switching Efficiency of Magnetic Tunnel Junctions by the Fieldlike Spin-Orbit Torque (2022)

Current-induced spin-orbit torques provide a versatile tool for switching magnetic devices. In perpendicular magnets, the dampinglike component of the torque is the main driver of magnetization reversal. The degree to which the fieldlike torque assists the switching is a matter of debate. Here we study the switching of magnetic tunnel junctions with a Co-Fe-B free layer and either $\mathrm{W}$ or $\mathrm{Ta}$ underlayers, which have a ratio of fieldlike to dampinglike torque of 0.3 and 1, respectively. We show that the fieldlike torque can either assist or hinder the switching of Co-Fe-B when the static in-plane magnetic field required to define the polarity of spin-orbit torque switching has a component transverse to the current. In particular, the noncollinear alignment of the field and current can be exploited to increase the switching efficiency and reliability compared with the standard collinear alignment. By probing individual switching events in real time, we also show that the combination of transverse magnetic field and fieldlike torque can accelerate or decelerate the reversal onset. We validate our observations using micromagnetic simulations and extrapolate the results to materials with different torque ratios. Finally, we propose device geometries that leverage the fieldlike torque for density increase in memory applications and synaptic weight generation.
Li-Ion Electrolytes Containing Ester Co-Solvents for Wide Operating Temperature Range (2008)

As part of our continuing efforts to develop advanced electrolytes to improve the performance of lithium-ion cells, especially at low temperatures, we have identified a number of electrolyte co-solvents that can be incorporated into multi-component electrolyte formulations for enhanced performance, especially at very low temperatures (down to -70oC). In the current work, we investigated a number of ester co-solvents, namely methyl propionate (MP), ethyl propionate (EP), methyl butyrate (MB), ethyl butyrate (EB), propyl butyrate (PB), and butyl butyrate (BB), in multi-component electrolytes of the following composition: 1.0 M LiPF6 in ethylene carbonate (EC) + ethyl methyl carbonate (EMC) + X (20:60:20 v/v %) [where X = ester co-solvent]. These electrolytes have been optimized to provide good low temperature performance (down to -60oC) while still offering reasonable high temperature resilience to produce the desired wide operating temperature systems (-60 to +60oC). This has primarily been achieved by fixing the EC-content at 20% and the ester co-solvent at 20%, in contrast to the previously developed systems.
Bacterial secreted proteins are required for the internalization of <i>Campylobacter jejuni</i> into cultured mammalian cells (1999)

Presented here is the first evidence that Campylobacter jejuni secrete proteins upon co-cultivation with host cells and in INT 407 cell-conditioned medium. A C. jejuni gene designated ciaB for Campylobacter invasion antigen B was identified, using a differential screening technique, which is required for this secretion process and the efficient entry of this bacterium into a host cell. The C. jejuni ciaB gene encodes a protein of 610 amino acids with a calculated molecular mass of 73 154 Da. The deduced amino acid sequence of the CiaB protein shares similarity with type III secreted proteins associated with the invasion of host cells from other more extensively characterized bacterial pathogens. In vitro binding and internalization assays revealed that the binding of C. jejuni ciaB null mutants was indistinguishable from that of the parental isolate, whereas a significant reduction was noted in internalization. Confocal microscopic examination of C. jejuni-infected cells revealed that CiaB was translocated into the cytoplasm of the host cells. Culturing C. jejuni with INT 407 cells or in INT 407-conditioned medium resulted in the secretion of at least eight proteins, ranging in size from 12.8 to 108 kDa, into the culture medium. C. jejuni ciaB null mutants were deficient in the secretion of all eight proteins, indicating that CiaB is required for the secretion process. The identification of the C. jejuni ciaB gene represents a significant advance in understanding the molecular mechanism of C. jejuni internalization and the pathogenesis of C. jejuni-mediated enteritis.
Structural and functional conservation of histidinol dehydrogenase between plants and microbes. (1991)

The partial amino acid sequence of histidinol dehydrogenase (L-histidinol:NAD+ oxidoreductase, EC 1.1.1.23) from cabbage was determined from peptide fragments of the purified protein. The relative positions of these peptides were deduced by aligning their sequences with the sequence of the HIS4C gene product of Saccharomyces cerevisiae. cDNA encoding histidinol dehydrogenase was then amplified from a library using a polymerase chain reaction primed with degenerate oligonucleotide pools of known position and orientation. By using this amplified fragment as a probe, an apparently full-length cDNA clone was isolated that is predicted to encode a proenzyme having a putative 31-amino acid chloroplast transit peptide and a mature molecular mass of 47.5 kDa. The predicted protein sequence was 51% identical to the yeast enzyme and 49% identical to the Escherichia coli enzyme. Expression of the cDNA clone in an E. coli his operon deletion strain rendered the mutant able to grow in the presence of histidinol.
Dihydropyrimidine dehydrogenase pharmacogenetics in Caucasian subjects (1998)

The five mutations analysed in this study are insufficient for identification of patients at risk for 5FU toxicity or thymine uraciluria. Both the splice site mutation and deltaC1897 are relatively rare in the general Caucasian population. Therefore, identification of further molecular alterations is required to facilitate the use of DPD analysis in genetic diagnosis and cancer therapeutics.
Honeycomb-Fin Heat Sink (1989)

Improved finned heat sink for electronic components more lightweight, inexpensive, and efficient. Designed for use with forced air, easily scaled up to dissipate power up to few hundred watts. Fins are internal walls of aluminum honeycomb structure. Cell structure gives strength to thin aluminum foil. Length of channels chosen for thermodynamic efficency; columns of cells combined in any reasonable number because flowing air distributed to all. Heat sink cools nearly as effectively at ends as near its center, no matter how many columns of cells combined.
Enabling node repair in any erasure code for distributed storage (2011)

Erasure codes are an efficient means of storing data across a network in comparison to data replication, as they tend to reduce the amount of data stored in the network and offer increased resilience in the presence of node failures. The codes perform poorly though, when repair of a failed node is called for, as they typically require the entire file to be downloaded to repair a failed node. A new class of erasure codes, termed as regenerating codes were recently introduced, that do much better in this respect. However, given the variety of efficient erasure codes available in the literature, there is considerable interest in the construction of coding schemes that would enable traditional erasure codes to be used, while retaining the feature that only a fraction of the data need be downloaded for node repair. In this paper, we present a simple, yet powerful, framework that does precisely this. Under this framework, the nodes are partitioned into two types and encoded using two codes in a manner that reduces the problem of node-repair to that of erasure-decoding of the constituent codes. Depending upon the choice of the two codes, the framework can be used to avail one or more of the following advantages: simultaneous minimization of storage space and repair-bandwidth, low complexity of operation, fewer disk reads at helper nodes during repair, and error detection and correction.
Software integrity protection using timed executable agents (2006)

We present a software scheme for protecting the integrity of computing platforms using Timed Executable Agent Systems (TEAS). A trusted challenger issues an authenticated challenge to a perhaps corrupt responder. New is that the issued challenge is an executable program that can potentially compute any function on the responder. The responder must compute not only the correct value implied by the agent, but also must complete this computation within time bounds prescribed by the challenger. Software-based attestation schemes have been proposed before---new capabilities introduced in TEAS provide means to mitigate the existing shortcomings of such proposed techniques. TEAS are general and can be adapted to many applications for which system integrity is to be tested.