gebhart/patrepeval huggingface dataset:
Transcriptional Regulation of the nadA Gene in Neisseria meningitidis Impacts the Prediction of Coverage of a Multicomponent Meningococcal Serogroup B Vaccine (2012)

The NadA adhesin is a major component of 4CMenB, a novel vaccine to prevent meningococcus serogroup B (MenB) infection. Under in vitro growth conditions, nadA is repressed by the regulator NadR and poorly expressed, resulting in inefficient killing of MenB strains by anti-NadA antibodies. Interestingly, sera from children infected with strains that express low levels of NadA in laboratory growth nevertheless recognize the NadA antigen, suggesting that NadA expression during infection may be different from that observed in vitro. In a strain panel covering a range of NadA levels, repression was relieved through deleting nadR. All nadR knockout strains expressed high levels of NadA and were efficiently killed by sera from subjects immunized with 4CMenB. A selected MenB strain, NGP165, mismatched for other vaccine antigens, is not killed by sera from immunized infants when the strain is grown in vitro. However, in an in vivo passive protection model, the same sera effectively protected infant rats from bacteremia with NGP165. Furthermore, we identify a novel hydroxyphenylacetic acid (HPA) derivative, reported by others to be produced during inflammation, which induces expression of NadA in vitro, leading to efficient antibody-mediated killing. Finally, using bioluminescent reporters, nadA expression in the infant rat model was induced in vivo at 3 h postinfection. Our results suggest that during infectious disease, NadR repression is alleviated due to niche-specific signals, resulting in high levels of NadA expression from any nadA-positive (nadA(+)) strain and therefore efficient killing by anti-NadA antibodies elicited by the 4CMenB vaccine.
End-host architecture for QoS-adaptive communication (2002)

Proliferation of communication-intensive real-time applications with "elastic" timeliness constraints such as streaming stored video, requires a new design for end-host communication subsystems. The design should (i) provide per-flow or per-service-class guarantees, (ii) maximize the aggregate utility of the communication service across all clients, (iii) gracefully adapt to transient overload, and (iv) avoid, if possible, starving lower-priority service classes during the period of sustained overload. The authors propose a QoS-optimization algorithm and communication subsystem architecture that satisfy the above requirements. It provides each client its contracted QoS, while adapting gracefully to transient overload and resource shortage. A new concept of flexible QoS contract is introduced, specifying multiple acceptable levels of service (or QoS levels for short) and their corresponding rewards for each client. Allowing clients to specify multiple QoS levels permits the server to perform QoS-optimization and degrade client's QoS under transient overload predictable, as specified in the QoS contract. Clients receive a money-back guarantee if the contracted QoS is violated by the server. The proposed resource-management mechanism maximizes server's total reward under resource constraints. They implemented and evaluated the architecture on a Pentium-based PC platform running under The Open Group (TOG) MK7.2 kernel, demonstrating the capability of the communication subsystem in meeting its design goals.
P1‐155: DIFFERENCES IN THE AMYLOID PLAQUE PROTEOME IN DOWN SYNDROME (2019)

The development of Alzheimer's disease (AD) neuropathology is inevitable in aged people with Down Syndrome (DS). Therefore, studying the molecular changes that occur in DS prior to the development of AD neuropathology provides an excellent opportunity to understand the factors that drive preclinical AD. However, our current knowledge of the factors that drive AD pathology in DS is incomplete and we do not fully know the similarities or differences in the molecular mechanisms that contribute to the development of AD neuropathology in DS and AD. Therefore, the aim of this study was to examine the proteome of amyloid plaques and cortex in cases of DS with AD neuropathology, AD, and age-matched controls to determine if there were protein expression differences. Protein differences were examined in cases of DS with AD neuropathology (n=5; age= 52.6±8.9yrs), AD (n=5; age=60.6±3.4yrs), and cognitively normal controls (n=5; age=56.2±1.9yrs). Unbiased, localized proteomics was used to specifically analyse the proteome of amyloid plaques or temporal cortex. Fluorescent immunohistochemistry was used to examine levels of total Aß, pyroglutamate Aß, Aß phosphorylated at serine 8, oligomeric species, and phosphorylated tau. Proteomic analysis resulted in the simultaneous quantification of 1650 proteins. Comparison of the plaque proteome in DS and AD revealed that while similar proteins were present in DS and AD plaques, the relative abundance of many key proteins were distinct in DS. For example, ApoE and Aß were 5.11 and 2.89 fold higher in DS plaques respectively. Network analysis suggested that DS plaques were particularly abundant in proteins related to the inflammatory response, the most notable difference being observed for HLA class II histocompatibility antigen (8.01 fold higher in DS vs AD plaques). Immunohistochemistry showed that DS plaques also contained a significantly higher amount of post-translationally modified Aß species than AD plaques including significantly higher amounts of Aß phosphorylated at serine 8 (p<0.05) and pyroglutamate modified Aß (p<0.001). Conversely, we observed significantly lower levels of oligomeric species in the DS cortex in comparison to the AD cortex (p<0.01). Our data suggests that there are key differences in the amyloid plaque proteome in DS and AD.
ChemInform Abstract: An Unusual Hydroxyl Inversion Mediated by DAST. (1990)

Abstract Cromakalim (Ia), which possesses a potent smooth‐muscle‐relaxant activity, as well as the similar compound (Ib) react with diethylaminosulfur trifluoride to form only the isomeric alcohols (IIa) and (IIb) instead of the expected fluorides.
Development and Validation of Confocal Endomicroscopy Diagnostic Criteria for Low-Grade Dysplasia in Barrett's Esophagus (2019)

We have generated and validated pCLE criteria for LGD in BE. Using these criteria, pCLE diagnosis of LGD is reproducible and has a substantial interobserver agreement.
Reproducibility and intratumoral heterogeneity of the PAM50 breast cancer assay (2023)

The PAM50 assay achieved very high technical reproducibility for breast cancer subtyping and ROR-P, but intratumoral heterogeneity is revealed by the assay in a small proportion of cases.
An overview of next-generation mobile WiMAX technology (2009)

The growing demand for mobile Internet and wireless multimedia applications has motivated the development of broadband wireless access technologies in recent years. Mobile WiMAX has enabled convergence of mobile and fixed broadband networks through a common wide-area radio-access technology and flexible network architecture. Since January 2007, the IEEE 802.16 working group has been developing a new amendment of the IEEE 802.16 standard (i.e., IEEE 802.16m) as an advanced air interface to meet the requirements of ITU-R/IMT-advanced for 4G systems, as well as for the next-generation mobile network operators. Depending on the available bandwidth and multi-antenna mode, the next-generation mobile WiMAX will be capable of over-the-air data-transfer rates in excess of 1 Gb/s and of supporting a wide range of high-quality and high-capacity IP-based services and applications while maintaining full backward compatibility with the existing mobile WiMAX systems to preserve investments and continuing to support first-generation products. This tutorial describes the prominent technical features of IEEE 802.16m and the potential for successful deployment of the next generation of mobile WiMAX in 2011+.
Thermochemical study of amino acid imprinted polymer films (2015)

Molecularly imprinted polymers provide an alternative to traditional methods of amino acid analysis. The imprinted polymers are more robust and significantly less expensive than, for example, ELISA analysis. Amino acid imprinted nylon-6 thin films were studied by differential scanning calorimetry and scanning electron microscopy. Endothermic peaks were observed for imprinted films at temperatures higher than that for pure nylon, indicating the formation of a more-ordered, hydrogen bonded polymer. Removal of the amino acid from the imprinted film resulted in reversion to the peak observed for pure nylon-6. Additives, β-cyclodextrin and multiwalled carbon nanotubes, were added to the imprinted polymer solutions as a means to increase the porosity of the films. These studies resulted in alternative morphologies and calorimetric results that provide additional functionalities and applications for imprinted polymers.
Glykanové profilování sér pacientek s rakovinou vaječníku senzitivních na léčbu platinovými deriváty (2015)

Východiska: Glykanove profilovani se zabýva se analýzou glykanů (oligosacharidových struktur). Změny v glykanovem profilu hraji důležitou roli v biologických i biochemických procesech v těle a soucasně mohou informovat o vzniku onemocněni připadně jeho progresi. Diagnozu ´rakovina vajecniku´ si každorocně vyslechne teměř ctvrt milionu žen a 140 000 ji rocně podlehne, což z ni cini sedmou nejcastějsi rakovinou u žen na světě. Chemoterapeuticka lecba platinovými derivaty představuje stale jednu z nejucinnějsich variant lecby, ale casto dochazi ke vzniku rezistence na platinove derivaty, kterou neni možne před podanim lecby zjistit. Material a metody: Pro studii byly pacientky vybrany na zakladě nasledujicich kriterii: při operaci bylo ponechano reziduum, charakter nadoru byl serozni a pacientky vykazovaly při lecbě senzitivitu nebo rezistenci na derivaty platiny. Pro glykanove profilovani bylo použito 2,5µl sera od pěti pacientek senzitivnich na lecbu platinovými derivaty srovnane s pěti sery odebiranými při preventivnich prohlidkach. Glykanove profilovani zahrnovalo denaturaci proteinů v seru, stěpeni, purifikaci glykanů přes grafitove kolonky, permethylaci byla nasledně usnadněna ionizace glykanů. Vzorky byly dale měřeny hmotnostnim spektrometrem MALDI TOF/TOF MS (Apllied Biosystems) v reflektorovem modu. Ziskana data byla normalizovana a statisticky vyhodnocena za použiti jednorozměrne ANOVY. Výsledky: Po statistickem vyhodnoceni dat z hmotnostnich spekter byly nalezeny 4 signifikantně odlisne glykanove struktury s efektivni hmotnosti 1922,9933 m/z (p<0,0033), 2097,0825 m/z (p<0,006), 2260,1558 m/z (p<0,01) a 2662,3560 m/z (p<0,0005). Soucasně bylo nalezeno 6 dalsich glykanových struktur jejichž statisticke odchylky se pohybuji v rozmezi p<0,091-0,08 což je řadi k dalsim potencialně nadějným strukturam. Zavěr:Výsledky studie obsahuji statisticky významně odlisných glykanových struktur nalezených v serech pacientek s nadorem vajecniku. Tato studie bude pokracovat analýzou glykanových struktur v serech pacientek rezistentnich na lecbu platinovými derivaty. Ziskane výsledky budou validovany na větsich souborech pacientek. V budoucnosti na tomto poznani bude možne adekvatně indikovat lecbu u pacientek, ktere z ni budou jednoznacně profitovat a na straně druhe nepodavat lecbu v připadech kdy ucinna nebude. Výsledky prace budou mit přimý dopad na běžnou klinickou praxi. Prace byla podpořena Evropským fondem pro regionalni rozvoj a statnim rozpoctem Ceske republiky (OP VaVpI - RECAMO CZ.1.05/2.1.00/03.0101), statnim rozpoctem Ceske republiky (LO1413) a MZ CR - RVO (MOU, 00209805) a IGA NT/13794-4/2012.
Cr(VI) Removal from Wastewater by Using Rice Husk Ash (RHA) (2006)

Rice husk ash (RHA) was studied as a potential adsorbent for Chromium (VI)removal from wastewater. RHA was able to remove effectively and economically toxic metal from synthetic wastewater. Experiments were done on the removal of Cr(VI) from dichromate solution which is a form of chromium in tannery effluent. The amount of Cr(VI) adsorption increased with the decrease in pH. The optimum parameter was = 2.0 evaluated at pH and the dose rate of the adsorbent was 5 kg RHNm3. The equilibrium data fit well in both the Langmuir and Freundlich isotherms. The study showed that 89.29 x 10-3kg Cr(VI) could be removed by 1 Kg of RHA. Since rice husk (RH) is available and cheap in Bangladesh, it can be used easily as an appropriate adsorbent to remove more than 95% Cr(VI) from tannery wastewater.
Cultura política y desigualdad en los consejos municipales de Curitiba (2004)

Este artículo estudia a los integrantes de los consejos gestores de políticas públicas en Curitiba, Brasil. Inicialmente se observa que los consejeros poseen, en relación con el conjunto de la población brasileña, una disponibilidad mayor de recursos de cultura política y de incentivos a la actividad política. Después se analizan dos cuestiones teóricas relativas a la cultura política: el problema de la relación de causalidad existente entre esas instituciones y la cultura política de sus miembros, y la cultura política como un recurso desigualmente distribuido entre los grupos que componen las instituciones analizadas y que representa una de las bases de la desigualdad política en el interior de la sociedad brasileña.
Actuation of liquid crystal elastomers reprocessed with carbon nanoparticles (2006)

Liquid crystal elastomers are currently of great interest due to their large thermally stimulated changes in shape. Here the authors show that by using an existing network and conducting carbon nanoparticles dispersed in a solvent with high swelling capability, a surface integrated layer can be created. This layer allows the effective resistivity to be reduced from highly insulating to usable values for electrical actuation and withstands large changes in geometrical shape both in contraction and expansion. Utilizing a resistive “Joule” heating effect, the reprocessed system shows a 150% length change and can be cycled beyond 10kcycles.
Optimization analysis of feedforward power amplifier (2003)

The efficiency optimization of a feedforward low distortion power amplifier is presented. Based on the principle of distortion compensation, the main amplifier output power, that of subamplifier, and amplifier efficiency have been accurately derived. In the present analysis, the coupling coefficient of main signal and distortion paths is selected as the optimization parameter because it may essentially affect the amplifier performance. Simulation results have been obtained for different values of signal cancel ratio and adjacent channel leakage power. The analysis contributes to the design improvement of a power amplifier of mobile communication base stations.
Patients With One Resurfacing and One Replacement Hip Show Which Hip Functions Better Without Selection Bias (2018)

INTRODUCTIONA recent PRCT failed to demonstrate superiority of HRA over THA at low speeds. Having seen HRA walk much faster, we wondered if faster walking speed might reveal larger differences.We t...
Dynamic detection of inter-application communication vulnerabilities in Android (2015)

A main aspect of the Android platform is Inter-Application Communication (IAC), which enables reuse of functionality across apps and app components via message passing. While a powerful feature, IAC also constitutes a serious attack surface. A malicious app can embed a payload into an IAC message, thereby driving the recipient app into a potentially vulnerable behavior if the message is processed without its fields first being sanitized or validated. We present what to our knowledge is the first comprehensive testing algorithm for Android IAC vulnerabilities. Toward this end, we first describe a catalog, stemming from our field experience, of 8 concrete vulnerability types that can potentially arise due to unsafe handling of incoming IAC messages. We then explain the main challenges that automated discovery of Android IAC vulnerabilities entails, including in particular path coverage and custom data fields, and present simple yet surprisingly effective solutions to these challenges. We have realized our testing approach as the IntentDroid system, which is available as a commercial cloud service. IntentDroid utilizes lightweight platform-level instrumentation, implemented via debug breakpoints (to run atop any Android device without any setup or customization), to recover IAC-relevant app-level behaviors. Evaluation of IntentDroid over a set of 80 top-popular apps has revealed a total 150 IAC vulnerabilities — some already fixed by the developers following our report — with a recall rate of 92% w.r.t. a ground truth established via manual auditing by a security expert.
Synthetic Studies on Hemicalide: Development of a Convergent Approach toward the C1–C25 Fragment (2013)

Synthetic studies on hemicalide, a recently isolated marine natural product displaying highly potent antiproliferative activity and a unique mode of action, have highlighted a reliable Horner-Wadsworth-Emmons olefination to create the C6-C7 alkene and a remarkable efficient Suzuki-Miyaura coupling to form the C15-C16 bond, resulting in the development of a convergent approach toward the C1-C25 fragment.
Intraoperative quantitative tremor evaluation in deep brain stimulation surgery (2016)

Poster
Architecture and methodology of a SoPC with 3.25Gbps CDR based SERDES and 1Gbps dynamic phase alignment (2004)

The SoPC (system on a programmable chip) aspects of the Stratix GX/spl trade/ FPGA with 3.125 Gbps SERDES are described. The FPGA was fabricated on a 0.13 /spl mu/m, 9-layer metal process. The 16 high-speed serial transceiver channels with clock data recovery (CDR) provides 622-Megabits per second (Mbps) to 3.125-Gbps full-duplex transceiver operation per channel. Another challenge described is the implementation of 39 source-synchronous channels at 100 Mbps to 1 Gbps, utilizing dynamic phase alignment (DPA). The implementation and integration of the FPGA logic array (with its own hard IP) with the CDR and DPA channels involved grappling with SoC design issues and methodologies.
How to Debug Inclusivity Bugs? A Debugging Process with Information Architecture (2022)

Although some previous research has found ways to find inclusivity bugs (biases in software that introduce inequities), little attention has been paid to how to go about fixing such bugs. Without a process to move from finding to fixing, acting upon such findings is an ad-hoc activity, at the mercy of the skills of each individual developer. To address this gap, we created Why/Where/Fix, a systematic inclusivity debugging process whose inclusivity fault localization harnesses Information Architecture(IA)-the way user-facing information is organized, structured and labeled. We then conducted a multi-stage qualitative empirical evaluation of the effectiveness of Why/Where/Fix, using an Open Source Software (OSS) project's infrastructure as our setting. In our study, the OSS project team used the Why/Where/Fix process to find inclusivity bugs, localize the IA faults behind them, and then fix the IA to remove the inclusivity bugs they had found. Our results showed that using Why/Where/Fix reduced the number of inclusivity bugs that OSS newcomer participants experienced by 90%. Diverse teams have been shown to be more productive as well as more innovative. One form of diversity, cognitive diversity - differences in cognitive styles - helps generate diversity of thoughts. However, cognitive diversity is often not supported in software tools. This means that these tools are not inclusive of individuals with different cognitive styles (e.g., those who like to learn through process vs. those who learn by tinkering), which burdens these individuals with a cognitive “tax” each time they use the tool. In this work, we present an approach that enables software developers to: (1) evaluate their tools, especially those that are information-heavy, to find “inclusivity bugs”- cases where diverse cognitive styles are unsupported, (2) find where in the tool these bugs lurk, and (3) fix these bugs. Our evaluation in an open source project shows that by following this approach developers were able to reduce inclusivity bugs in their projects by 90%.
Relationship between Plasma Ghrelin, Insulin, Leptin, IL6, Adiponectin, Testosterone and Longevity in the Baltimore Longitudinal Study of Aging (2011)

Background and aims: Caloric restriction (CR) is the most robust and reproducible intervention for slowing aging, and maintaining health and vitality in animals. Previous studies found that CR is associated with changes in specific biomarkers in monkeys that were also associated with reduced risk of mortality in healthy men. In this study we examine the association between other potential biomarkers related to CR and extended lifespan in healthy humans. Methods: Based on the Baltimore Longitudinal Study of Aging, "long-lived" participants who survived to at least 90 years of age (n=41, cases) were compared with "short-lived" participants who died between 72–76 yrs of age (n=31, controls) in the nested case control study. Circulating levels of ghrelin, insulin, leptin, interleukin 6, adiponectin and testosterone were measured from samples collected between the ages 58 to 70 yrs. Baseline differences between groups were examined with t-test or Wilcoxon test, and mixed effects general linear model was used for a logistic model to differentiate the two groups with multiple measurements on some subjects. Results: At the time of biomarkers evaluation (58–70 yrs), none of the single biomarker levels was significantly different between the two groups. However, after combining information from multiple biomarkers by adding the z-transformed values, the global score differentiated the long- and short-lived participants (p=0.05). Conclusions: In their sixties, long-lived and short-lived individuals do not differ in biomarkers that have been associated with CR in animals. However, difference between the groups was only obtained when multiple biomarker dysregulation was considered.
Spur-free all-digital PLL in 65nm for mobile phones (2011)

After the first-ever all-digital PLL (ADPLL) [1] for Bluetooth radios has proven benefits of CMOS scaling and integration, demonstrators for more challenging wireless standards have emerged [2-6]. In the ADPLL, however, the digitally controlled oscillator (DCO) and time-to-digital converter (TDC) quantize the time and frequency tuning functions, respectively, which can lead to spurious tones and phase noise increase. As such, finite TDC resolution can distort data modu lation and spectral mask at near integer-N channels, while finite DCO step size can add far-out spurs and phase noise. Also, a major underreported issue is an injection pulling of the DCO due to harmonics of the digital activity at closely spaced frequencies, which can also create spurs. This work addresses all these problems and demonstrates RF performance matching that of the best-in-class traditional approaches.