gebhart/patrepeval huggingface dataset:
Energy-Efficient Power Loading for a MIMO-SVD System and Its Performance in Flat Fading (2010)

In this paper we formulate a power loading problem for the spatial subchannels (parallel channels) of a single-carrier MIMO-SVD system. The power loading solution is designed to minimize the energy-per-goodbit (EPG) of the MIMO-SVD system. The optimum power loading obtained by solving a nonlinear fractional program, has a closed-form expression and is found by applying a water-filling procedure. It is observed that the optimum total transmit power (water level) depends not only on the MIMO channel realization, but also on the ratio of circuit power cost (which depends on the number of antennas) to transmit power cost (which depends on path loss and other factors). We study the statistical performance (using simulation) of the solution in Rayleigh and Rician flat-fading channels. Using outage EPG as a measure of performance, we determine the MIMO configuration (from a set of allowed configurations) that yields the minimum outage EPG. It is observed that the average number of spatial subchannels utilized (which indicates preference for diversity or multiplexing) depends on the ratio of circuit power cost to transmit power cost and fading type (Rayleigh or Rician). For both cases, the results show that both multiplexing and diversity obtained by MIMO systems are critical for energy efficiency.
Data Poisoning Attacks Against Federated Learning Systems (2020)

Federated learning (FL) is an emerging paradigm for distributed training of large-scale deep neural networks in which participants' data remains on their own devices with only model updates being shared with a central server. However, the distributed nature of FL gives rise to new threats caused by potentially malicious participants. In this paper, we study targeted data poisoning attacks against FL systems in which a malicious subset of the participants aim to poison the global model by sending model updates derived from mislabeled data. We first demonstrate that such data poisoning attacks can cause substantial drops in classification accuracy and recall, even with a small percentage of malicious participants. We additionally show that the attacks can be targeted, i.e., they have a large negative impact only on classes that are under attack. We also study attack longevity in early/late round training, the impact of malicious participant availability, and the relationships between the two. Finally, we propose a defense strategy that can help identify malicious participants in FL to circumvent poisoning attacks, and demonstrate its effectiveness.
Femtosecond laser written integrated photonics on sapphire (2023)

This paper presents the compact integration of photonics devices on a sapphire chip in the telecommunications waveband. The devices include waveguides, a waveguide array, a directional coupler and a splitter.
Reading and writing omes (2013)

Mol Syst Biol. 9: 642

‘Systems Technologies’ are increasingly potent drivers of biological research. Molecular Systems Biology will be illustrating this evolution with a new Reviews Series highlighting key technologies in systems medicine, genome‐scale, computational, quantitative and synthetic biology. The series is launched with a review from the Snyder group on reading human omes (Soon et al , 2013) and a companion review on writing genomes from Harvard's Wyss Institute (Esvelt and Wang, 2013).

Exponential improvement in reading and writing technologies (Carr and Church, 2009) (1.5‐fold/year since 1960s, 6‐fold per year since 2005) created a series of breakthroughs: The first genome read was MS2 in 1976 (phiX in 1977); first written was hepatitis C virus in 2000 (Blight et al, 2000) (polio in 2002). The first bacterial genome read was Helicobacter in 1994 ( Haemophilus in 1995). The first genome transplanted from in vitro DNA into radically foreign cytoplasm was Synechocystis into Bacillus in 2005 (then Mycoplasma mycoides into similar cytoplasm in 2007). Significantly, so far, no vertebrate genome has been fully read, due to repetitive regions, and no new organism function has been achieved by genome‐scale writing. We expect to see breakthroughs on both fronts in 2013.

The first widely used genetic engineering vector was pBR322, constructed and sequenced 1977‐1978, parts of which are still present in modern vectors. This enabled dissection of previously recalcitrant biological systems via pure …
The FUT2 Variant c.461G>A (p.Trp154*) Is Associated With Differentially Expressed Genes and Nasopharyngeal Microbiota Shifts in Patients With Otitis Media (2022)

Otitis media (OM) is a leading cause of childhood hearing loss. Variants in <i>FUT2</i>, which encodes alpha-(1,2)-fucosyltransferase, were identified to increase susceptibility to OM, potentially through shifts in the middle ear (ME) or nasopharyngeal (NP) microbiotas as mediated by transcriptional changes. Greater knowledge of differences in relative abundance of otopathogens in carriers of pathogenic variants can help determine risk for OM in patients. In order to determine the downstream effects of <i>FUT2</i> variation, we examined gene expression in relation to carriage of a common pathogenic <i>FUT2</i> c.461G>A (p.Trp154*) variant using RNA-sequence data from saliva samples from 28 patients with OM. Differential gene expression was also examined in bulk mRNA and single-cell RNA-sequence data from wildtype mouse ME mucosa after inoculation with non-typeable <i>Haemophilus influenzae</i> (NTHi). In addition, microbiotas were profiled from ME and NP samples of 65 OM patients using 16S rRNA gene sequencing. In human carriers of the <i>FUT2</i> variant, <i>FN1, KMT2D, MUC16</i> and <i>NBPF20</i> were downregulated while <i>MTAP</i> was upregulated. Post-infectious expression in the mouse ME recapitulated these transcriptional differences, with the exception of <i>Fn1</i> upregulation after NTHi-inoculation. In the NP, Candidate Division TM7 was associated with wildtype genotype (FDR-adj-<i>p</i>=0.009). Overall, the <i>FUT2</i> c.461G>A variant was associated with transcriptional changes in processes related to response to infection and with increased load of potential otopathogens in the ME and decreased commensals in the NP. These findings provide increased understanding of how <i>FUT2</i> variants influence gene transcription and the mucosal microbiota, and thus contribute to the pathology of OM.
On Geometric and Algebraic Aspects of 3D Affine and Projective Structures from Perspective 2D Views (1993)

Part I of this paper investigates the di erences | conceptually and algorithmically | b e t ween a ne and projective frameworks for the tasks of visual recognition and reconstruction from perspective views.It is shown that an a ne invariant exists between any view and a xed view chosen as a reference view.This implies that for tasks for which a reference view can be chosen, such as in alignment s c hemes for visual recognition, projective i n variants are not really necessary.The projective extension is then derived, showing that it is necessary only for tasks for which a reference view is not available | such as happens when updating scene structure from a moving stereo rig.The geometric di erence between the two proposed invariants are that the a ne invariant measures the relative deviation from a single reference plane, whereas the projective i n variant measures the relative deviation from two reference planes.The a ne invariant can be computed from three corresponding points and a fourth point for setting a scale the projective i n variant can be computed from four corresponding points and a fth point for setting a scale.Both the a ne and projective i n variants are shown to be recovered by r e m a r k ably simple and linear methods.In part II we use the a ne invariant t o d e r i v e new algebraic connections between perspective views.It is shown that three perspective views of an object are connected by certain algebraic functions of image coordinates alone (no structure or camera geometry needs to be involved).In the general case, three views satisfy a trilinear function of image coordinates.In case where two of the views are orthographic and the third is perspective the function reduces to a bilinear form.In case all three views are orthographic the function reduces further to a linear form (the \linear combination of views" of 31]).These functions are shown to be useful for recognition, among other applications.
Nanozyme-amplified lateral flow immunoassay for molecular signature detection of cardiovascular diseases (2019)

Point-of-care (PoC) devices offer the opportunity to decentralize the analysis of biomarkers in biological fluids thus&#13;\nproviding patients with more personalized medicine. The golden standard of PoC platforms are lateral flow assays&#13;\nsince they are low cost, quick to perform and user-friendly [1]. Here we show the use of a nanozyme-mediated&#13;\nsignal readout on a multiplexed PoC lateral flow immunoassay for the diagnosis of cardiovascular diseases. Our&#13;\naim has been to expand the application of this ultrasensitive detection method towards the development of a&#13;\nmultiplexed PoC assay for cardiovascular-related biomarkers to support triage of myocardial injury.
Motion artifacts in standard clinical setting obscure disease-specific differences in quantitative susceptibility mapping (2018)

As quantitative susceptibility mapping (QSM) is maturing, more clinical applications are being explored. With this comes the question whether QSM is sufficiently robust and reproducible to be directly used in a clinical setting where patients are possibly not cooperative and/or unable to suppress involuntary movements sufficiently. Twenty-nine patients with Alzheimer's disease, 31 patients with mild cognitive impairment and 41 healthy controls were scanned on a 3 T scanner, including a multi-echo gradient-echo sequence for QSM and an inversion-prepared segmented gradient-echo sequence (T1-TFE, MPRAGE). The severity of motion artifacts (excessive/strong/noticeable/invisible) was categorized via visual inspection by two independent raters. Quantitative susceptibility was reconstructed using 'joint background-field removal and segmentation-enhanced dipole inversion', based on segmented subcortical gray-matter regions, as well as using 'morphology enabled dipole inversion'. Statistical analysis of the susceptibility maps was performed per region. A large fraction of the data showed motion artifacts, visible in both magnitude images and susceptibility maps. No statistically significant susceptibility differences were found between groups including motion-affected data. Considering only subjects without visible motion, significant susceptibility differences were observed in caudate nucleus as well as in putamen. Motion-effects can obscure statistically significant differences in QSM between patients and controls. Additional measures to restrict and/or compensate for subject motion should be taken for QSM in standard clinical settings to avoid risk of false findings.
Construction and Properties of Replication-Competent Murine Retroviral Vectors Encoding Methotrexate Resistance (1989)

A series of replication-competent Moloney murine leukemia virus vectors was constructed in which each vector contained a mutant dihydrofolate reductase (DHFR) cDNA insert in the U3 region of the viral long terminal repeat. Two of the resulting viruses, MLV (murine leukemia virus) DHFR*-5 and MLV DHFR*-7, were able to stably transfer methotrexate resistance to infected fibroblast cells upon multiple rounds of virus replication and in the absence of drug selection. Cell lines producing recombinant virus with high titers were established, which indicated that the insert did not grossly interfere with viral replication functions. These vectors should be useful for introducing and expressing foreign genes in vivo in tissues and whole animals in which virus spread is needed for efficient infection.
Wrinkle in the plan: miR-34a-5p impacts chemokine signaling by modulating CXCL10/CXCL11/CXCR3-axis in CD4+, CD8+ T cells, and M1 macrophages (2020)

MiR-34a-5p mimic administered by intravenous administration will likely not only be up-taken by the tumor cells but also by the immune cells. Our results indicate that miR-34a-5p over-expression leads in M1 macrophages to a reduced secretion of CXCL10 and CXCL11 chemokines and in CD4<sup>+</sup> and CD8<sup>+</sup> T cells to a reduced expression of CXCR3. As a result, less immune cells will be attracted to the tumor site. Furthermore, high levels of miR-34a-5p in naive CD4<sup>+</sup> T cells can in turn hinder Th1 cell polarization through the downregulation of CXCR3 leading to a less pronounced activation of cytotoxic T lymphocytes, natural killer, and natural killer T cells and possibly contributing to lymphocytopenia.
Blue‐Emitting Heteroleptic Iridium(III) Complexes Suitable for High‐Efficiency Phosphorescent OLEDs (2007)

Dyed-in-the-wool true blue: True-blue phosphorescent organic light-emitting diodes are fabricated by using an IrIII dopant (see picture; gray C; blue N; red Ir; green F). The Ir complex has an enhanced metal-to-ligand charge-transfer contribution, hence a shortened radiative lifetime in the excited state. The maximum external quantum efficiency of the fabricated device is 8.5 % and the main emission is around 450 nm. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z604733_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Sound-Power Flow—A Practitioner's Handbook for Sound Intensity (2017)

First Page
Muscarinic M4 and M5 receptors in the ventral subiculum differentially modulate alcohol seeking versus consumption in male alcohol‐preferring rats (2021)

Collectively, our data highlight alcohol-induced cholinergic dysregulation in the vSub and distinct roles for M<sub>4</sub> and M<sub>5</sub> receptor allosteric modulators to reduce alcohol consumption or seeking.
Chemical-Induced Inhibition of Blue Light-Mediated Seedling Development Caused by Disruption of Upstream Signal Transduction Involving Cryptochromes inArabidopsis thaliana (2016)

Plants have a remarkable ability to perceive and respond to various wavelengths of light and initiate regulation of different cascades of light signaling and molecular components. While the perception of red light and the mechanisms of its signaling involving phytochromes are largely known, knowledge of the mechanisms of blue light signaling is still limited. Chemical genetics involves the use of diverse small active or synthetic molecules to evaluate biological processes. By combining chemicals and analyzing the effects they have on plant morphology, we identified a chemical, 3-bromo-7-nitroindazole (3B7N), that promotes hypocotyl elongation of wild-type Arabidopsis only under continuous blue light. Further evaluation with loss-of-function mutants confirmed that 3B7N inhibits photomorphogenesis through cryptochrome-mediated light signaling. Microarray analysis demonstrated that the effect of 3B7N treatment on gene expression in cry1cry2 is considerably smaller than that in the wild type, indicating that 3B7N specifically interrupts cryptochrome function in the control of seedling development in a light-dependent manner. We demonstrated that 3B7N directly binds to CRY1 protein using an in vitro binding assay. These results suggest that 3B7N is a novel chemical that directly inhibits plant cryptochrome function by physical binding. The application of 3B7N can be used on other plants to study further the blue light mechanism and the genetic control of cryptochromes in the growth and development of plant species.
Postoperative neuroimaging analysis of DRT deep brain stimulation revision surgery for complicated essential tremor (2017)

Our work underpins a possible superiority of direct targeting approaches using advanced neuroimaging technologies to perform personalized DBS surgery. The evaluation of DBS electrode positions with the herein-described neuroimaging simulation technologies will likely improve targeting and revision strategies. Direct targeting with DTI FT-assisted approaches in a variety of indications is the focus of our ongoing research.
Enhancing Text-based Reinforcement Learning Agents with Commonsense\n Knowledge (2020)

In this paper, we consider the recent trend of evaluating progress on\nreinforcement learning technology by using text-based environments and games as\nevaluation environments. This reliance on text brings advances in natural\nlanguage processing into the ambit of these agents, with a recurring thread\nbeing the use of external knowledge to mimic and better human-level\nperformance. We present one such instantiation of agents that use commonsense\nknowledge from ConceptNet to show promising performance on two text-based\nenvironments.\n
IMC-EB10, an Anti-FLT3 Monoclonal Antibody, Prolongs Survival and Reduces Nonobese Diabetic/Severe Combined Immunodeficient Engraftment of Some Acute Lymphoblastic Leukemia Cell Lines and Primary Leukemic Samples (2006)

The class III receptor tyrosine kinase FLT3 is expressed on the blasts of >90% of patients with B-lineage acute lymphoblastic leukemias (ALL). In addition, it is expressed at extremely high levels in ALL patients with mixed lineage leukemia rearrangements or hyperdiploidy and is sometimes mutated in these same patients. In this report, we investigate the effects of treating ALL cell lines and primary samples with human anti-FLT3 monoclonal antibodies (mAb) capable of preventing binding of FLT3 ligand. In vitro studies, examining the ability of two anti-FLT3 mAbs (IMC-EB10 and IMC-NC7) to affect FLT3 activation and downstream signaling in ALL cell lines and primary blasts, yielded variable results. FLT3 phosphorylation was consistently inhibited by IMC-NC7 treatment, but in some cell lines, IMC-EB10 actually stimulated FLT3 activation, possibly as a result of antibody-mediated receptor dimerization. Through antibody-dependent, cell-mediated cytotoxicity, such an antibody could still prove efficacious against leukemia cells in vivo. In fact, IMC-EB10 treatment significantly prolonged survival and/or reduced engraftment of several ALL cell lines and primary ALL samples in nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice. This occurred even when IMC-EB10 treatment resulted in FLT3 activation in vitro. Moreover, fluorescence-activated cell sorting and PCR analysis of IMC-EB10-treated NOD/SCID mice surviving 150 days post-leukemic cell injection revealed that FLT3 immunotherapy reduced leukemic engraftment below the level of detection in these assays (<0.001%). Furthermore, in vivo IMC-EB10 treatment did not select for resistant cells, because cells surviving IMC-EB10 treatment remain sensitive to IMC-EB10 cytotoxicity upon retransplantation. In vivo studies involving either partial depletion or activation of natural killer (NK) cells show that most of the cytotoxic effect of IMC-EB10 is mediated through NK cells. Therefore, such an antibody, either naked or conjugated to radioactive isotopes or cytotoxic agents, may prove useful in the therapy of infant ALL as well as childhood and adult ALL patients whose blasts typically express FLT3.
X-ray CT observation of pore structures of porous metal fabricated by sintering and dissolution process and its mechanical properties (2017)

Functionally graded porous aluminum (Al) was fabricated by spark plasma sintering process. In this process, the mixture of Al alloy powder, TiH2 powder and Al2O3 powder (powder I) and the mixture of pure Al powder and sodium chloride (NaCl) powder as spacer particle (powder II) were used as starting materials. The powder mixtures were sintered by spark plasma sintering. Pores were formed by foaming and dissolution process. In this study, pore structures of obtained porous Al were nondestructively observed by X-ray computing tomography (CT).
Guanine-containing ssDNA and RNA induce dimeric and tetrameric SAMHD1 in cryo-EM and binding studies (2023)

The dNTPase activity of tetrameric SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) plays a critical role in cellular dNTP regulation. SAMHD1 also associates with stalled DNA replication forks, DNA repair foci, ssRNA, and telomeres. The above functions require nucleic acid binding by SAMHD1, which may be modulated by its oligomeric state. Here we establish that the guanine-specific A1 activator site of each SAMHD1 monomer is used to target the enzyme to guanine nucleotides within single-stranded (ss) DNA and RNA. Remarkably, nucleic acid strands containing a single guanine base induce dimeric SAMHD1, while two or more guanines with ~20 nucleotide spacing induce a tetrameric form. A cryo-EM structure of ssRNA-bound tetrameric SAMHD1 shows how ssRNA strands bridge two SAMHD1 dimers and stabilize the structure. This ssRNA-bound tetramer is inactive with respect to dNTPase and RNase activity.
Identifying and Targeting Sporadic Oncogenic Genetic Aberrations in Mouse Models of Triple-Negative Breast Cancer (2017)

Triple-negative breast cancers (TNBC) are genetically characterized by aberrations in <i>TP53</i> and a low rate of activating point mutations in common oncogenes, rendering it challenging in applying targeted therapies. We performed whole-exome sequencing (WES) and RNA sequencing (RNA-seq) to identify somatic genetic alterations in mouse models of TNBCs driven by loss of <i>Trp53</i> alone or in combination with <i>Brca1</i> Amplifications or translocations that resulted in elevated oncoprotein expression or oncoprotein-containing fusions, respectively, as well as frameshift mutations of tumor suppressors were identified in approximately 50% of the tumors evaluated. Although the spectrum of sporadic genetic alterations was diverse, the majority had in common the ability to activate the MAPK/PI3K pathways. Importantly, we demonstrated that approved or experimental drugs efficiently induce tumor regression specifically in tumors harboring somatic aberrations of the drug target. Our study suggests that the combination of WES and RNA-seq on human TNBC will lead to the identification of actionable therapeutic targets for precision medicine-guided TNBC treatment.<b>Significance:</b> Using combined WES and RNA-seq analyses, we identified sporadic oncogenic events in TNBC mouse models that share the capacity to activate the MAPK and/or PI3K pathways. Our data support a treatment tailored to the genetics of individual tumors that parallels the approaches being investigated in the ongoing NCI-MATCH, My Pathway Trial, and ESMART clinical trials. <i>Cancer Discov; 8(3); 354-69. ©2017 AACR.</i><i>See related commentary by Natrajan et al., p. 272</i><i>See related article by Matissek et al., p. 336</i><i>This article is highlighted in the In This Issue feature, p. 253</i>.
Selective Electrochemical Trimethylsilylation of Tetrachlorocyclopropene to 1-(Trimethylsilyl)-trichlorocyclopropene, a New Cyclopropene Building Block1 (1994)

A new efficient procedure for the selective trimethylsilylation of readily available tetrachlorocyclopropene is described. The electrochemical silylation gave the title compound 2 on a preparative scale in 78% yield. Ionization of 2 to its corresponding cyclopropenium ion and its functionalization by treatment with arenes is described. The properties of the title compound were also investigated.