gebhart/patrepeval huggingface dataset:
Coordinated Regulation of SIV Replication and Immune Responses in the CNS (2009)

Central nervous system (CNS) invasion during acute-stage HIV-infection has been demonstrated in a small number of individuals, but there is no evidence of neurological impairment at this stage and virus infection in brain appears to be controlled until late-stage disease. Using our reproducible SIV macaque model to examine the earliest stages of infection in the CNS, we identified immune responses that differentially regulate inflammation and virus replication in the brain compared to the peripheral blood and lymphoid tissues. SIV replication in brain macrophages and in brain of SIV-infected macaques was detected at 4 days post-inoculation (p.i.). This was accompanied by upregulation of innate immune responses, including IFNbeta, IFNbeta-induced gene MxA mRNA, and TNFalpha. Additionally, IL-10, the chemokine CCL2, and activation markers in macrophages, endothelial cells, and astrocytes were all increased in the brain at four days p.i. We observed synchronous control of virus replication, cytokine mRNA levels and inflammatory markers (MHC Class II, CD68 and GFAP) by 14 days p.i.; however, control failure was followed by development of CNS lesions in the brain. SIV infection was accompanied by induction of the dominant-negative isoform of C/EBPbeta, which regulates SIV, CCL2, and IL6 transcription, as well as inflammatory responses in macrophages and astrocytes. This synchronous response in the CNS is in part due to the effect of the C/EBPbeta on virus replication and cytokine expression in macrophage-lineage cells in contrast to CD4+ lymphocytes in peripheral blood and lymphoid tissues. Thus, we have identified a crucial period in the brain when virus replication and inflammation are controlled. As in HIV-infected individuals, though, this control is not sustained in the brain. Our results suggest that intervention with antiretroviral drugs or anti-inflammatory therapeutics with CNS penetration would sustain early control. These studies further suggest that interventions should target HIV-infected individuals with increased CCL2 levels or HIV RNA in the CNS.
On the structural anisotropy of sands (2020)

In this paper the results of undrained triaxial tests performed on the Hostun RF sand are presented. It has been observed that the sand response is very sensitive to the type of load applied (compression or extension under monotonic or cyclic loading) resulting in very different conclusions concerning the analysis of stability. It will be shown that the analysis of the effective stress paths in the p’-q diagram can offer a meaningful tool for assessing the material anisotropy.
Analysis of genomic data from high throughput sequencing: concepts and basic methods (2011)

International audience
Association between serum copper levels and cervical cancer risk: a meta-analysis (2018)

Whether serum copper levels were higher in patients with cervical cancer than that in controls was controversial. Hence, we conducted the present study to explore the relationship between serum copper levels and cervical cancer. We searched PubMed, WanFang, and China National Knowledge Internet (CNKI) for relevant studies before November 30, 2017. Standardized mean difference (SMD) and 95% confidence interval (CI) were used to combine results across studies using the random-effect model. A total of 14 publications involving 747 patients with cervical cancer and 1014 controls were eligible through inclusion criteria. In comparison with controls, serum copper levels were significantly higher in patients with cervical cancer [summary SMD = 1.35; 95%CI: 0.10-2.59], with significant heterogeneity (<i>I<sup>2</sup></i> = 98.8%; <i>P</i><0.001) was found. Significant association was also found among Asian populations [summary SMD = 1.39; 95%CI: 0.06-2.71]. The association was positive in subgroup analysis of population-based case-control studies (PBCC) [summary SMD = 1.64; 95%CI: 0.02-3.34], but not in hospital-based case-control studies (HBCC). Through a sensitivity analysis, we did not identify any single study to strongly influence the results of our serum copper levels and cervical cancer risk. No publication bias was found in our analysis. In conclusion, our study provided significant evidence of higher serum copper levels in patients with cervical cancer than in controls, suggesting that serum copper exposure was a risk factor on cervical cancer.
Liver tumor imaging: current concepts. (1990)

With the increasing availability of curative surgical techniques for primary and secondary hepatic neoplasms, the tasks for clinical imaging of patients suspected of having liver cancer have become more exacting. Detection of tumor, differential diagnosis of individual nodules, and mapping the anatomic extensions of malignant disease are now required routinely. Related and unrelated liver substrate abnormalities such as cavernous hemangioma and focal fatty deposits are often discovered in these patients and must be differentiated from metastatic deposits. Moreover, modern imaging methods frequently display tiny nodules (less than 1 cm) that often prove difficult to adequately characterize (micrometastases vs other kinds of lesions). The most sensitive imaging techniques are CT after arterial portography and intraoperative sonography, but because of their invasiveness, these are reserved exclusively for cancer staging. For primary screening, MR imaging is increasingly preferred over CT because of its superiority in discriminating hemangiomas and cysts from metastases without the need for iodinated contrast material.
Supplementary Figure Legend from Ganitumab (AMG 479) Inhibits IGF-II–Dependent Ovarian Cancer Growth and Potentiates Platinum-Based Chemotherapy (2023)

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Overcoming Barriers to Health Service Access and Influencing the Demand Side Through Purchasing (2004)

This paper investigates the role of demand-side barriers in impeding access to the use of health services. Demand-side barriers are defined as determinants of use of health care that are not dependent on service delivery or price or direct price of those services. They include distance, education, opportunity cost, and cultural and social barriers. There is some evidence that these barriers are at least as important in determining access to services as the quality, volume, and price of services delivered by health care providers. The paper is divided into two sections. In the first section literature on demand barriers to accessing services is reviewed. Since the literature on these barriers is so substantial, the review is restricted to an illustrative survey of the main barriers in low-, middle-, and high-income countries. The second section surveys studies that report and evaluate methods for overcoming these barriers. The literature here is substantially less voluminous even when gray and unpublished sources are included in the survey. Many of the studies relate to access to obstetrical and family planning care. In most cases evaluation is not rigorous, and it is often hard to separate the impact of the intervention itself from other confounding factors. Few of the studies reported have an explicit poverty focus, although many of the interventions are conducted in poor areas. There is a clear need for further work to examine the most cost effective ways of reducing barriers to accessing services and in particular to investigate what methods are most effective in expanding access to essential care among the poor.
Dendritic L‐type calcium currents in mouse spinal motoneurons: implications for bistability (2000)

The intrinsic properties of mammalian spinal motoneurons provide them with the capability to produce high rates of sustained firing in response to transient inputs (bistability). Even though it has been suggested that a persistent dendritic calcium current is responsible for the depolarizing drive underlying this firing property, such a current has not been demonstrated in these cells. In this study, calcium currents are recorded from functionally mature mouse spinal motoneurons using somatic whole-cell patch-clamp techniques. Under these conditions a component of the current demonstrated kinetics consistent with a current originating at a site spatially segregated from the soma. In response to step commands this component was seen as a late-onset, low amplitude persistent current whilst in response to depolarizing-repolarizing ramp commands a low voltage clockwise current hysteresis was recorded. Simulations using a neuromorphic motoneuron model could reproduce these currents only if a noninactivating calcium conductance was placed in the dendritic compartments. Pharmacological studies demonstrated that both the late-onset and hysteretic currents demonstrated sensitivity to both dihydropyridines and the L-channel activator FPL-64176. Furthermore, the alpha1D subunits of L-type calcium channels were immunohistochemically demonstrated on motoneuronal dendrites. It is concluded that there are dendritically located L-type channels in mammalian motoneurons capable of mediating a persistent depolarizing drive to the soma and which probably mediate the bistable behaviour of these cells.
Double‐stimuli‐responsive degradable hydrogels: interpenetrating polymer networks consisting of gelatin and dextran with different phase separation (1996)

Abstract Biodegradable interpenetrating polymer network (IPN)‐structured hydrogels consisting of gelatin (Gtn) and dextran (Dex) were prepared by sequential crosslinking reactions of Gtn and methacryloylated Dex. Phase separation of these hydrogels is dominated by preparation conditions, i.e., above or below the sol‐gel transition temperature ( T trans ) of Gtn. Enzymatic degradation by either α‐chymotrypsin or dextranase is hindered for the IPN‐structured hydrogel prepared below T trans whereas this hydrogel is perfectly degradable in the presence of both enzymes. Such a specific feature of enzymatic degradation was not observed for the hydrogel prepared above T trans . These results suggest that double‐stimuli‐responsive degradation of IPN‐structured hydrogels is related to their phase separation.
Variations in gene organization and DNA uptake signal sequence in the folP region between commensal and pathogenic Neisseria species (2006)

Genetic recombination events immediately upstream of folP and horizontal transfer have resulted in sequence differences in the folP region between the Neisseria species. This variability could be a consequence of the selective pressure on this region exerted by the use of sulfonamide drugs.
Advances in LDL-apheresis for the treatment of severe hypercholesterolemia (1994)

LDL-apheresis is an extracorporeal plasma-perfusion method that selectively removes apolipoprotein B-containing lipoproteins from the blood. It is indicated for patients with homozygous and drug-resistant heterozygous familial hypercholesterolemia. Clinical and angiographic regression of coronary artery disease has been demonstrated in patients treated with cholesterol-lowering programs that include LDL-apheresis.
Antenna-coupled millimeter-wave electro-optical modulators (2002)

As the modulation frequency is increased in a traveling wave electro-optic modulator, good performance becomes more and more difficult to realize. There are generally three reasons for this: (1) velocity mismatch, (2) electrode loss, and (3) parasitic inductance and capacitance in the connections to the electrodes. Several schemes have been invented to deal with these limitations, some of which have already been discussed in Chapter 5. In this chapter we introduce a new scheme that offers improvement in all three limiting aspects, but is practical only at very high microwave frequencies. The basic scheme is simple. The transmission line electrodes of the modulator are broken into N sections, and each section is connected to an on-substrate antenna. The array of antennas thus formed is excited by a plane wave incident from the substrate side, as illustrated in Fig. 11.1. The illumination angle is chosen so that the phase velocity from antenna to antenna is the same as the phase velocity of the light in the optical waveguide. This assures velocity matching from segment to segment, even though the phase velocities of RF and optical waves are not matched within a segment. This overcomes limitation (1), so that the modulator may be made as long as desired. While the optical power is now divided by N (at best), the attenuation along each segment is now α L/N compared to α L for a simple modulator of length L with transmission line loss of α nepers/unit length.
Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA (2015)

https://bioinf.eva.mpg.de/schmutzi/ license:GPLv3.
NKX6.3 protects against gastric mucosal atrophy by downregulating β-amyloid production (2019)

NKX6.3 inhibits gastric mucosal atrophy by regulating Aβ accumulation and inflammatory reaction in gastric epithelial cells.
German-Russian Catholic Colonization in Western Kansas: a Settlement Geography. (1970)

The success that this researcher has had in achieving his objectives is due, in large measure, to the understanding and kind assistance of the German-Russian informants of Ellis and Rush dounties, Kansas. Without the aid of these people, this study would have been impossible and it should be noted that in the many months of field research, not one individual was approached who refused to be interviewed at length.
Negative dispersion of birefringence of smectic liquid crystal-polymer composite: dependence on the constituent molecules and temperature (2015)

We investigated the dependence of the negative dispersion of birefringence of smectic liquid crystal-polymer composites on the constituent molecules and temperature. The dispersion of birefringence was significantly varied from positive dispersion to negative dispersion by the change of the relative fraction of the constituent monomers. For the temperature dependence of the dispersion, a composite with more fraction of monomers located at the inter-layer space showed a wider temperature range of the negative dispersion of birefringence.
Characterization of Trap States at Silicon-On-Insulator (SOI)/Buried Oxide (BOX) Interface by Back Gate Transconductance Characteristics in SOI MOSFETs (2003)

We characterized trap states at silicon-on-insulator (SOI)/buried oxide (BOX) interfaces in epitaxial layer transfer (ELTRAN) wafers and in low-dose separation by implanted oxygen (SIMOX) wafers. We formulated a simple analytical form to obtain the distribution of density of trap states from a comparison of the experimental transconductance and simulated transconductance of SOI metal oxide semiconductor field effect transistors (MOSFETs). We observed dips in back gate transconductance in MOSFETs on low-dose SIMOX wafers. Consequently, we concluded that "acceptor-like electron traps" with the density of 5 ×1012 cm-2·eV-1 near the conduction band edge Ec and "donor-like hole traps" with the density of 1012 cm-2·eV-1 near the valence band edge Ev are distributed in the forbidden band of Si at SOI/BOX interfaces in low-dose SIMOX wafers, while the trap density at SOI/BOX interfaces is less than 1011 cm-2·eV-1 in ELTRAN wafers. We also found that the kink effect is suppressed in MOSFETs on low-dose SIMOX wafers with a high density of trap states at the SOI/BOX interface.
Palladium-Catalyzed Direct Ethynylation of C(sp3)–H Bonds in Aliphatic Carboxylic Acid Derivatives (2011)

The first catalytic alkynylation of unactivated C(sp(3))-H bonds has been accomplished. The method allows for the straightforward introduction of an ethynyl group into aliphatic acid derivatives under palladium catalysis. This new reaction can be applied to the rapid elaboration of complex aliphatic acids, for example, via azide/alkyne cycloaddition.
Investigation of Carbon-based Label-Free Electrochemical Aptasensors for Point-of-Care Cancer Biomarker Detection (2021)

Cancer is the second cause of death, with millions of fatalities every year. The early detection of cancer can tremendously increase the survival chances of the patients. An effective approach for early detection of cancer is developing reliable and relatively cheap biosensors that can quantify the cancer biomarkers from blood samples. These classes of the biosensor are commonly referred to as point-of-care (POC) cancer biomarker biosensors. The label-free electrochemical biosensors based on carbon dravite materials can be feasible for POC cancer biomarker biosensors. The present dissertation aims to design, develop, and optimize carbon-based biosensors for label-free detection of lactic acid and platelet-derived growth factor-BB (PDGF-BB) cancer biomarkers. Two carbon-based materials are used for developing the biosensor: carbon-micro electrotechnical systems (aka. C-MEMS) and bipolar exfoliated graphene. In the first phase of this dissertation, enzymatic biosensors based on interdigitated C-MEMS microelectrodes were investigated. The achieved results confirmed that the C-MEMS-based sensing platform functionalized with oxygen-plasma treatment could provide a stable sensing system with low background noise, which can be used for label-free detection. In the next phase of the dissertation, for the first time, the C-MEMS electrode functionalized with oxygen-plasma was adopted for ssDNA aptamer-based biosensors (aka. aptasensors). The attained results confirmed that the developed aptasensors are highly sensitive, selective, and robust, and the developed system is adaptable for turn-on and turn-off sensing strategies. In the following phase of the dissertation, the adaptability of the bipolar exfoliated graphene for aptasensors was investigated. The achieved results revealed that the graphene deposited on a negative feeding electrode (i.e., reduced graphene oxide) is more suitable for label-free electrochemical aptasensing. Hence, POC PDGF-BB aptasensors based on bipolar reduced graphene oxide were developed and investigated for the first time. The achieved results were highly promising for feasible POC cancer aptasensors. The last phase of this dissertation explores the in-situ integration of bipolar exfoliated graphene on C-MEMS microelectrodes. The biosensor developed based on this integration showed enhanced sensitivity. In the present dissertation, novel carbon-based biosensors were developed and optimized. The achieved results show the high potential of C-MEMS and bipolar exfoliated graphene-based biosensors for label-free POC cancer biomarker biosensing.
Temperature Effect on 1H Chemical Shift of Hydroxyl Groups in Zeolites and Their Catalytic Activities as Solid Acids (2012)

The influence of temperature on the 1H chemical shift due to hydroxyl groups in H+-exchanged any kind of zeolites (ZSM-5 type zeolites including silicalite, mordenite and Y zeolites) was examined by variable temperature 1H magic-angle spinning nuclear magnetic resonance (1H MAS NMR) spectroscopy measured from 298 to 673 K. The 1H chemical shifts due to bridging hydroxyl groups (Si–(OH)–Al, Brönsted acid sites), which have a lower activation energy for proton jumping, terminal silanol groups, and nest silanol groups increased with temperature. The temperature dependence of the 1H chemical shift due to the bridging hydroxyl groups was more pronounced than that due to the terminal silanol groups and also the nest silanol groups. The relationship between the 1H chemical shift and the acid strength of the hydroxyl groups in zeolites was discussed on the basis of the variable temperature 1H MAS NMR measurements of zeolites, previously reported thermal analysis data, such as the heat of NH3 adsorption measured by NH3 temperature-programmed desorption, and also the catalytic activity for the conversion of ethanol and 1-hexene. It was found that the nest silanol groups of silicalite functioned as Brönsted acid sites and could catalyze the conversion of ethanol and 1-hexene with the same activity as the bridging hydroxyl groups in B-ZSM-5 at 673 K.
ESPnet: End-to-End Speech Processing Toolkit (2018)

This paper introduces a new open source platform for end-to-end speech processing named ESPnet. ESPnet mainly focuses on end-to-end automatic speech recognition (ASR), and adopts widely-used dynamic neural network toolkits, Chainer and PyTorch, as a main deep learning engine. ESPnet also follows the Kaldi ASR toolkit style for data processing, feature extraction/format, and recipes to provide a complete setup for speech recognition and other speech processing experiments. This paper explains a major architecture of this software platform, several important functionalities, which differentiate ESPnet from other open source ASR toolkits, and experimental results with major ASR benchmarks.
Biofuels: Biomolecular Engineering Fundamentals and Advances (2010)

The biological production of fuels from renewable sources has been regarded as a feasible solution to the energy and environmental problems in the foreseeable future. Recently, the biofuel product spectrum has expanded from ethanol and fatty acid methyl esters (biodiesel) to other molecules, such as higher alcohols and alkanes, with more desirable fuel properties. In general, biosynthesis of these fuel molecules can be divided into two phases: carbon chain elongation and functional modification. In addition to natural fatty acid and isoprenoid chain elongation pathways, keto acid-based chain elongation followed by decarboxylation and reduction has been explored for higher alcohol production. Other issues such as metabolic balance, strain robustness, and industrial production process efficiency have also been addressed. These successes may provide both scientific insights into and practical applications toward the ultimate goal of sustainable fuel production.
Competitividade industrial brasileira e o papel das capacidades tecnológicas inovadoras: a necessidade de uma investigação criativa (2016)

Este documento objetiva apresentar alguns dos principais aspectos da abordagem, do desenho edos métodos do projeto de pesquisa intitulado: “Acumulação de Capacidades Tecnológicas e Fortalecimento da Competitividade Industrial no Brasil: Análise Empírica e Recomendações Práticas para Políticas Públicas e Estratégias Empresariais.”
Crosswalk Detection Using Dynamic Bayesian Network Based on Analyzing Edge Pattern (2010)

This paper proposes a novel crosswalk detection technique for self-localization of automobile. The self-localization function based on the proposed technique can estimate highly accurate self-position by comparing results of image recognition with positions of crosswalks in map database. This paper focuses on a robust method to detect a crosswalk and its reference point which is used to calculate the distance between the self-position of host vehicle and the crosswalk. Our method can detect crosswalks and reference points from rear camera image sequences in real time. The previous road marking detection techniques hardly detect crosswalks with robustness because the rear camera images have some noise such as damages of road markings, halation, and shadows. Our method estimates the state including rough relative position of the crosswalk by Dynamic Bayesian Network in order to detect crosswalks and reference points robustly. The proposed method uses also the specification of crosswalk to reduce computational cost. The proposed method was tested on real images to confirm the accuracy and computational cost. The experimental results show that our method can detect crosswalks with a high degree of stability in real time.
Lysins to kill - A tale of viral weapons of mass destruction (2011)

“Your mission should you choose to accept, is to locate the enemy, silently dock on the cell surface and inject the genetic blueprint. Once inside, you must then hijack the host’s cellular machinery and assemble multiple clones. Working quickly then, slice open the cell wall perimeter and escape to repeat the process on the remaining enemy hosts” Although farfetched, this passage describes the efficient killing machinery of bacteriophages, and depicts the events which occur millions of times in nature every day as bacteria succumb to their tiny deadly nemeses.