gebhart/patrepeval huggingface dataset:
Select high risk genetic features predict earlier progression following chemotherapy in chronic lymphocytic leukemia: Prospective randomized trial (Intergroup E2997) to evaluate justification for risk-adapted therapy (2006)

6521 Background: Genomic features including lack of IgV H mutations, del(11q), del(17p), and p53 mutations have been reported to predict clinical course and overall survival in CLL patients (pts). Bcl-2 family proteins and ZAP-70 have also been explored as predictors in CLL. Methods: We prospectively evaluated the prognostic significance of clinical features and laboratory variables on response and progression-free survival (PFS) following treatment with fludarabine (F, n=132) or fludarabine plus cyclophosphamide (FC, n=137) as part of the US Intergroup Trial E2997 for previously untreated CLL. Results: FC therapy had higher complete response (CR) (23.4% versus 4.6%), overall response (OR) (74.3% versus 59%), and median PFS (31.6 mos versus 19.2 mos) compared to F. CR and OR were not significantly different based on interphase cytogenetics, IgV H status, or p53 mutation. IgV H status or levels of ZAP-70, Bcl-2, Bax, Mcl-1, XIAP, Caspase-3, and Traf-1 proteins were not associated with clinical response or PFS. IgV H status and ZAP-70 levels were associated with time from diagnosis to treatment. Using a model including treatment arm, pts with del(17p) or (11q) had significantly shorter PFS (hazard ratios 3.54 and 2.05 respectively). In pts with a p53 mutation without del(17p) there was no enhancement of the model predicting poorer outcome, nor did IgV H status enter the model for predicting PFS. Conclusions: Combination chemotherapy is associated with a higher CR, OR, and PFS. Also, initiation of therapy for pts with Rai stages 0/1 resulted in a higher response rate. Del(17p) and del(11q) are highly predictive of shortened PFS with fludarabine-based chemotherapy. IgV H and p53 mutational status, as well as expression of ZAP-70, Bcl-2 family proteins, and CD38, did not predict response or PFS. ZAP-70 expression is associated with cytogenetic subsets predicted to have a worse overall prognosis, but did not identify pts who will do poorly with therapy. A combination of clinical staging and cytogenetics provide support for future risk-stratified treatment of CLL. Pts with a projected short response duration can be identified for future investigational strategies. No significant financial relationships to disclose.
Quantum‐resistant anonymous identity‐based encryption with trable identities (2021)

Abstract Identity‐based encryption (IBE), introduced by Shamir, eliminates the need for public‐key infrastructure. The sender can simply encrypt a message by using the recipient's identity (such as email or IP address) without needing to look up the public key. In particular, when ciphertexts of an IBE do not reveal recipient's identity, this scheme is known as an anonymous IBE scheme. Recently, Blazy et al. (ARES '19) analysed the trade‐off between public safety and unconditional privacy in anonymous IBE and introduced a new notion that incorporates traceability into anonymous IBE, called anonymous IBE with traceable identities (AIBET). However, their construction is based on the discrete logarithm assumption, which is insecure in the quantum era. In this paper, we first formalize the consistency of tracing key of the AIBET scheme to ensure that a ciphertext cannot be traced with the use of wrong tracing keys. Subsequently, we present a generic formulation concept that can be used to transform structure‐specific lattice‐based anonymous IBE schemes into an AIBET. Finally, we apply this concept to Katsumata and Yamada's compact anonymous IBE scheme (Asiacrypt '16) to obtain the first quantum‐resistant AIBET scheme that is adaptively secure under the ring learning with errors assumption without random oracle.
A note on Tinagma balteolella F.v.R. (Lep.: Douglasiidae) (1988)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Personal microbiomes and next-generation sequencing for laboratory-based education (2016)

Sequencing and bioinformatics technologies have advanced rapidly in recent years, driven largely by developments in next-generation sequencing (NGS) technology. Given the increasing importance of these advances, there is a growing need to incorporate concepts and practices relating to NGS into undergraduate and high school science curricula. We believe that direct access to sequencing and bioinformatics will improve the ability of students to understand the information obtained through these increasingly ubiquitous research tools. In this commentary, we discuss approaches and challenges for bringing NGS into the classroom based on our experiences in developing and running a microbiome project in high school and undergraduate courses. We describe strategies for maximizing student engagement through establishing personal relevance and utilizing an inquiry-based structure. Additionally, we address the practical issues of incorporating cutting edge technologies into an established curriculum. Looking forward, we anticipate that NGS educational experiments will become more commonplace as sequencing costs continue to decrease and the workflow becomes more user friendly.
A 5.5 mW ADPLL-Based Receiver With a Hybrid Loop Interference Rejection for BLE Application in 65 nm CMOS (2016)

This paper presents a low-power hybrid-loop receiver (RX) with high-interference tolerance for Bluetooth low energy (BLE). The hybrid-loop structure based on an all-digital phase-locked loop enables the RX to both enhance the interference tolerance and digitize the frequency-modulated signal without an ADC. A novel single channel receiving method, which enables the conversion of the constellation from frequency shift keying to differential binary phase shift keying signal, is adopted to eliminate the Q-channel signal processing to reduce the power consumption. The prototype RX fabricated in a 65 nm CMOS technology consumes only 5.5 mW and fulfills the BLE requirements of the adjacent channel rejection and out-of-band blocker tolerance without exception. The sensitivity level is -90 dBm.
Supplemental Table 2 from The Tyrosine Kinase Adaptor Protein FRS2 Is Oncogenic and Amplified in High-Grade Serous Ovarian Cancer (2023)

&lt;p&gt;Supplemental Table 2. List of genes contained in genomic region 12q15 (chr12: 69692322-71120515) that are recurrently amplified in high-grade serous ovarian cancers.&lt;/p&gt;
References (2008)

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Frequency Offset Estimation and Training Sequence Design for MIMO OFDM (2008)

This paper addresses carrier frequency offset (CFO) estimation and training sequence design for multiple-input multiple-output (MIMO) orthogonal frequency division multiplexing (OFDM) systems over frequency selective fading channels. By exploiting the orthogonality of the training sequences in the frequency domain, integer. CFO (ICFO) is estimated. With the uniformly spaced non-zero pilots in the training sequences and the corresponding geometric mapping, fractional CFO (FCFO) is estimated through the roots of a real polynomial. Furthermore, the condition for the training sequences to guarantee estimation identifiability is developed. Through the analysis of the correlation property of the training sequences, two types of sub-optimal training sequences generated from the Chu sequence are constructed. Simulation results verify the good performance of the CFO estimator assisted by the proposed training sequences.
Optical imaging in photodynamic therapy: mechanisms and applications (2004)

Molecular excitation of photosensitizing agents provides reactive excited states, which can initiate chemical reactions, but it can also lead to molecular relaxation via radiative photophysical processes, providing the basis for fluorescence diagnostics. The best-known example of the former is Photodynamic Therapy (PDT), which is now approved for the treatment of a number of neoplastic and non-neoplastic pathologies. Although the concept of the use of photodynamic agents in diagnostics is as old as their use in therapy, the focused development of this aspect has been relatively recent. Typically, photodynamic agents have high triplet yields and relatively long triplet lifetimes (microsecond range), which allows them to interact and destroy molecular targets near them either directly or indirectly by producing other toxic molecular species. Associated with a high triplet yield is the fortunate attribute of most PDT agents in having low but finite fluorescence quantum yields. Fluorescence from these molecules may be used not only for diagnostics of disease de novo but also for guided surgery, PDT dosimetry and therapeutic monitoring. Other uses of fluorescence in PDT (not necessarily from the PDT agents) include the development of technologies that allow tracking of cells during treatment in vivo, studies of sub-cellular localization of molecules for mechanistic studies and photosensitizer tracking for specific targeting. An overview of studies on these aspects from different laboratories will be presented.
Development of the M59TLB (2009)

&lt;div class="htmlview paragraph"&gt;Kubota's compact Tractor Loader Backhoe series are versatile machines that can be used not only for construction work such as digging or loading but also for rear implement work using the three point linkage and PTO. Kubota introduced the M59TLB as the top end model of this series. Kubota successfully increased the competitiveness of the M59TLB to make it a product which is acceptable even for the large TLB market. This success is the result of the technological achievements mentioned in this paper such as an electronically-controlled HST with a stall guard system, an auto-self leveling loader valve, control over the backhoe swing rushing phenomenon, and the crawling feature from the backhoe seat, strong loader dump force, and more.&lt;/div&gt;
Identification of sequences required for the import of human protoporphyrinogen oxidase to mitochondria (2004)

Protoporphyrinogen oxidase (PPOX; EC 1.3.3.4), the penultimate enzyme of haem biosynthesis, is a nucleus-encoded flavoprotein strongly associated with the outer surface of the inner mitochondrial membrane. It is attached to this membrane by an unknown mechanism that appears not to involve a membrane-spanning domain. The pathway for its import to mitochondria and insertion into the inner membrane has not been established. We have fused human PPOXs containing N-terminal deletions, C-terminal deletions or missense mutations to yellow fluorescent protein (YFP) and have used these constructs to investigate the mitochondrial import of PPOX in human cells. We show that all the information required for efficient import is contained within the first 250 amino acid residues of human PPOX and that targeting to mitochondria is prevented by fusion of YFP to the N-terminus. Deletion of between 151 and 175 residues from the N-terminus is required to abolish import, whereas shorter deletions impair its efficiency. Fully efficient targeting appears to require both a major targeting signal, the whole or part of which is contained between residues 151 and 175, and which may be involved in anchoring to the inner mitochondrial membrane, together with interaction between this region and a sequence(s) within the first 150 residues. These features suggest that the mechanism for import of human PPOX to mitochondria differs from those identified for the translocation of nucleus-encoded, membrane-spanning, inner membrane proteins. In addition, a missense mutation outside this region (Val(335)-->Gly) prevented targeting to mitochondria and delayed the appearance of YFP fluorescence. This mutation appeared to prevent import by a direct effect on protein folding rather than by altering a sequence required for targeting. It may lead to sequestration of the PPOX-YFP construct in an unfolded conformation, followed by proteolytic degradation, possibly through enhanced binding to a cytosolic chaperone protein.
Low-frequency acoustic scattering from a submerged bubble cloud. (1991)

A group of us has undertaken a series of measurements of the low-frequency scattering from a bubble cloud produced by a submerged bubble maker in Seneca Lake. Acoustic scattering from this cloud for a range of frequencies, for a number of different acoustic sources, and for a variety of cloud compositions and geometries has been examined. The latest results of these experiments will be reported. [Work supported in part by ONR, ONT, and AEAS.]
OMVPE grown 1.3 μm GaInNAs quantum well lasers (2003)

OMVPE grown GaInNAs quantum well lasers with low threshold current (density) of 14.5mA (330A/cm/sup 2/) at 1.24 /spl mu/m, and high power operation (>60mW) at 1.30 /spl mu/m have been achieved.
Exploitation of Harmonic Signals Backscattered by UHF RFID Tags : HRFID Project (2022)

International audience
BRCA1 CpG Island Hypermethylation Predicts Sensitivity to Poly(Adenosine Diphosphate)- Ribose Polymerase Inhibitors (2010)

Recently, Fong et al reported the antitumor activity of the poly(adenosine diphosphate)-ribose polymerase (PARP) inhibitor olaparib (AZD2281; KU-0059436) in patients with BRCA1/BRCA2 germline mutated ovarian cancer. Female BRCA1 and BRCA2 mutation carriers have a significantly elevated lifetime risk of breast and ovarian cancer. BRCA1 and BRCA2 proteins play major roles in DNA double-strand break repair through homologous recombination, and inhibition of DNA single-strand break repair leads to the accumulation of double-strand breaks. These potentially lethal events in homologous recombination-deficient cells could be exploited for therapeutic purposes. The PARP-1 protein is essential for single-strand break repair, and inhibition of PARP leads to persistence of DNA lesions normally repaired by homologous recombination.
SHADE: Automated Refinement of PCB Component Estimates Using Detected Shadows (2020)

Automated Visual Inspection (AVI) is an established approach for Printed Circuit Board (PCB) analysis. Several existing AVI methods have been well-developed for quality assurance, but not for hardware security and trust assessment. The main distinction between these two cases is that a golden sample (reference PCB) is available in the former application but is not guaranteed in the latter. Hence, conventional AVI approaches falsely detect many non-components (e.g. traces, vias, board text) as legitimate ones (e.g. resistors, capacitors, transistors). Such false detections cripple the scalability of hardware assurance approaches. In this paper, we propose an algorithm which exploits shadows cast by surface-mount components to accurately distinguish them from their invalid counterparts. It refines an initial component detection estimate by ruling out false positives. Moreover, the algorithm yields a per-component confidence metric which adds flexibility to the process' sensitivity threshold. Tests on a sample PCB indicate as many as half of the initial false positives from a component estimate can be removed while retaining 96% of the true positives.
E104 Identification of Three Distinct Epitope Regions in the V2 Portion of gp120 (2013)

Until recently, V2 was virtually overlooked as a target for vaccine development, but its potential importance as a vaccine target has recently emerged as a result of data from the RV144 HIV-1 vaccine efficacy trial showing that high levels of Abs specific for the V1/V2 region were correlated with a statistically significant reduction in the rate of HIV infection. Studies of various human V2 monoclonal Abs (mAbs) demonstrate that both polyclonal and monoclonal V2-specific Abs can be highly cross-reactive, display neutralizing activity, capture virus particles, mediate ADCC, and block gp120/4 7 interaction. Recent data show that the V1/V2 region harbors at least 3 distinct epitope regions as defined by the reactivity of various mAbs. (1) PG9, a mAb specific for a conformational epitope which includes portions of V1, V2, and V3, reacts with two glycans and amino acids in the B and C-strands of the 4-stranded -sheet domain assumed by V1/V2 when presented on a scaffold protein and bound to this mAb. (2) mAbs CH58 and CH59 react with linear V2 peptides. The epitopes recognized by these mAbs, which were derived from the cells of an RV144 vaccinee, consist of amino acids that map to the aforementioned C-strand in V2. (3) Seven additional mAbs (e.g., 697D) were developed from subjects with chronic HIV-1 infection; the epitopes recognized by these mAbs are highly conformation-dependent and target a discontinuous region in V2 which is located in a region between -strands C and D. The epitopes recognized by these latter mAbs map to a surface area clearly different from those recognized by CH58, CH59 and PG9. The current data thus indicate that there are at least three distinct types of V2 epitopes.
Induction of proline-rich proteins in hamster salivary glands by isoproterenol treatment and an unusual growth inhibition by tannins. (1987)

Treatment of hamsters with the beta-agonist isoproterenol caused a dramatic increase in a series of unusual proteins in the parotid and submandibular glands. These proteins are acid soluble and they contain high amounts (mol%) of glutamate plus glutamine (30-35), proline (23-30), and glycine (12-25). Three proteins (HP45, HP43a, and HP43b) were isolated from trichloroacetic acid extracts of parotid glands of isoproterenol-treated hamsters. The basic protein (HP45) was not retained by DEAE-cellulose and did not contain phosphate or carbohydrate. Two acidic proteins (HP43a and HP43b) had the same apparent molecular weight on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, but these were separated by DEAE-cellulose chromatography. HP43a and HP43b contained 4.3 and 5.7 phosphate residues/mol of protein, respectively. Levels of mRNAs encoding this series of proteins showed striking increases following isoproterenol treatment as determined by cell-free translations and Northern analysis. Feeding tannins to rats and mice mimicks the effects of isoproterenol treatment on the parotid gland (Mehansho, H., Hagerman, A., Clements, S., Butler, L., Rogler, J., and Carlson, D.M. (1983) Proc. Natl. Acad. Sci. U.S.A. 80, 3948-3952; Mehansho, H., Clements, S., Sheares, B. T., Smith, S., and Carlson, D. M. (1985) J. Biol. Chem. 260, 4418-4423]. However, hamsters on a high tannin diet (2%) did not respond like rats and mice and instead displayed an unusual growth inhibition. Weanling hamsters maintained on a 2% tannin diet initially lost weight for 3 days and then failed to gain weight for up to 6 months when kept on this diet. Essentially a normal growth rate was observed when the tannin-fed hamsters were switched to a normal diet.
Multistage metal hydride compressor (1986)

Metal hydride compressors can compress hydrogen to high pressures without using mechanical moving parts. They are particularly suited for tritium applications because they require minimal maintenance. A three-stage metal hydride compressor which can compress hydrogen from 14.7 to 20,000 psia has been demonstrated. The design principle and experimental results are presented.
Abstract TMP28: Inhibition of Integrin α 5 β 1 With the Small Peptide Atn-161 Reduces Infarct Volume and Improves Functional Recovery Through Reduction of Blood-brain Barrier Permeability (2018)

Reperfusion-induced injury after recanalization is exacerbated by blood-brain barrier (BBB) dysfunction after ischemic stroke. Endothelial cell integrin receptors, specifically the β 1 subtype, play a direct role in BBB dysfunction through regulation of barrier-forming tight junction (TJ) proteins. We hypothesize that inhibition of an endothelial specific β 1 integrin, α 5 β 1 , after oxygen-glucose deprivation (OGD) in vitro and also after experimental stroke in vivo will stabilize the BBB through the TJ claudin-5, reducing infarct volumes and improving functional recovery. First, stroke was simulated in vitro by OGD or TNF- α treatment of brain endothelial cell monolayers. Treatment with the small peptide α 5 β 1 inhibitor ATN-161 (10 μM) resulted in decreased barrier permeability as measured by trans-endothelial cell electrical resistance and FITC-dextran permeability. Immunocytochemistry showed extracellular localization and upregulation of claudin-5 with ATN-161 treatment. Next, transient tandem middle cerebral artery occlusion was performed on 12-week-old male mice for 1 hour. On confocal and SEM imaging, post-stroke α 5 β 1 expression was upregulated primarily in the luminal vascular surface by post-stroke day (PSD) 2 rather than at the basement membrane (next to its extracellular matrix ligands). IP injection of ATN-161 (1 mg/kg) immediately after reperfusion and on PSD 1, and PSD2 caused a significant, but transient and acute (after the initial dose only) change in animal pulse distension, but no change in body temperature or heart rate. Infarct volumes, measured by TTC stain, were significantly reduced in ATN-161 treated animals. Furthermore, BBB integrity was improved by ATN-161 as determined by IgG staining and FITC-Dextran injection. Functional recovery, assessed by a 5-item Neuroscore, was also significantly improved. In conclusion, inhibition of α 5 β 1 by ATN-161 was well tolerated, reduced infarct volume, and improved behavioral recovery. Additional studies showed this result was likely due to reduced BBB permeability through the TJ claudin-5. Therefore, inhibition of α 5 β 1 with ATN-161 could represent a novel therapeutic approach for stroke worthy of further investigation.
A new low complexity iterative equalization architecture for high-speed receivers on highly dispersive channels: Decision feedforward equalizer (DFFE) (2011)

This paper introduces the decision feedforward equalizer (DFFE), a new low complexity iterative equalization architecture for high speed receivers used on channels with large intersymbol interference (ISI). The decision feedback equalizer (DFE) is one of the preferred receivers for high ISI channels. The high data and symbol rate of current communications systems often require parallel processing receiver implementations [1]. Unfortunately, the complexity of parallel architectures of the DFE grows exponentially with the channel memory [2] and limits their application to low ISI channels. The DFFE avoids the exponential growth of the DFE by using tentative decisions to iteratively cancel the ISI. We show that the DFFE can achieve performance similar to the DFE. These benefits make it an excellent choice for high-speed receivers required to operate over highly dispersive channels.