gebhart/patrepeval huggingface dataset:
Functional characterization of Ih‐channel splice variants from Apis mellifera (2004)

We isolated splice variants of the AMIH cDNA by means of polymerase chain reaction and homology screening. Splicing at one site generates at least four different channel transcripts (AMIH, AMIHL, AMIHM and AMIHT), which code for ion-channel proteins that vary in the interloop regions between the membrane-spanning domains S4 and S5. HEK293 cells in which the AMIHL splice variants were functionally expressed generated currents that were activated by hyperpolarizing voltage steps. Compared to AMIH, AMIHL cells showed pronounced differences in the voltage dependency of activation: the incorporation of 32 extra amino acids between S4 and S5 shifts the activation curve by +25 mV. Intracellular cAMP made the current-activation potential still less negative and accelerated the activation more effectively than it does in AMIH cells. In vertebrates, functional diversity of Ih-channels is generated by four different genes. In Apis mellifera, splice variants coded by the single gene AMIH could generate a similar diversity.
Supplementary Data from Global Phosphoproteomics Reveal CDK Suppression as a Vulnerability to KRas Addiction in Pancreatic Cancer (2023)

&lt;p&gt;Supplementary Table 2&lt;/p&gt;
Elastic online analytical processing on RAMCloud (2013)

A shared-nothing architecture is state-of-the-art for deploying a distributed analytical in-memory database management system: it preserves the in-memory performance advantage by processing data locally on each node but is difficult to scale out. Modern switched fabric communication links such as InfiniBand narrow the performance gap between local and remote DRAM data access to a single order of magnitude. Based on these premises, we introduce a distributed in-memory database architecture that separates the query execution engine and data access: this enables a) the usage of a large-scale DRAM-based storage system such as Stanford's RAMCloud and b) the push-down of bandwidth-intensive database operators into the storage system. We address the resulting challenges such as finding the optimal operator execution strategy and partitioning scheme. We demonstrate that such an architecture delivers both: the elasticity of a shared-storage approach and the performance characteristics of operating on local DRAM.
Monophosphate as Eminent Ligand to Bind Ce(IV)/EDTA Complex for Site-selective DNA Hydrolysis (2004)

Abstract By the use of oligonucleotides bearing a terminal monophosphate, 10-base gap was formed in substrate DNA and the monophosphates were placed at the edge of gap. Upon the treatment of these systems with Ce(IV)/EDTA complex, the gap-site was selectively hydrolyzed. The monophosphates remarkably promoted both the selectivity and the efficiency of scission.
Enteroviruses and Type 1 Diabetes Mellitus: An Overlooked Relationship in Some Regions (2020)

Enteroviruses (EVs) infect millions of people annually. EV infections can be asymptomatic or symptomatic with conditions ranging from mild illnesses to serious diseases such as dilated cardiomyopathy. A causal relationship between EV infections and type 1 diabetes mellitus (T1DM) has been heavily debated, with some studies suggesting that this relationship is not yet conclusive and requires additional evidence, whereas others strongly argue for this correlation. While this relationship is well investigated in some developed countries like the USA and Finland, it is understudied or neglected in other countries like Russia for many reasons such as the low incidence of T1DM. Although the Middle East and North Africa (MENA) are highly affected by T1DM, the role of EVs in the disease in MENA has not been investigated extensively. Therefore, we aimed to address the relationship between T1DM and EVs in MENA and other regions globally.
Sinus floor augmentation with simultaneous placement of dental implants in the presence of platelet‐rich plasma or recombinant human bone morphogenetic protein‐7 (2004)

The aim of the present study was to evaluate the possible benefit of platelet-rich plasma (PRP) in sinus grafting as compared with recombinant human bone morphogenetic protein-7 (rhBMP-7). For this purpose, we performed a bilateral sinus augmentation with anorganic bovine bone and simultaneous insertion of a titanium screw implant in five miniature pigs. Six hundred microliters of PRP and 15%-vol. autologous bone, which was collected with a trap during preparation of the implant recipient site, were added to the right sinus and 420 microl rhBMP-7 to the left sinus. A polychrome sequential labeling was performed. The animals were sacrificed 6 weeks after surgery. Undecalcified ground sections were evaluated by microradiography, digitized histomorphometry and under fluorescent light. The mean bone-implant contact using rhBMP-7 was 45.8% and 5.7% under PRP (P=0.002). The mean height of newly mineralized bone in the augmented area using rhBMP-7 amounted to 8.3 mm as opposed to 3.6 mm under PRP (P=0.013). Using PRP, the mean area of the newly formed bone was enhanced (51.3%) as compared with rhBMP-7 (33.1%); however, this difference was not statistically significant (P=0.081). In conclusion, under the selected experimental conditions the use of rhBMP-7 led to superior outcomes with regard to the osseointegration of dental implants and the height of new bone as compared with the use of PRP.
Spatial resolution of ballistic electron emission microscopy measured on metal/quantum-well Schottky contacts (2005)

Au Schottky contacts on cleaved AlGaAs∕GaAs∕AlGaAs quantum wells (QWs) were used as precise nanometer-scale apertures to quantify the spatial resolution of ballistic electron emission microscopy (BEEM). Both the amplitude and width of the measured average BEEM current profiles showed systematic dependencies on the QW width and Au film thickness, indicating surprisingly large BEEM resolutions of ∼12, ∼16, and ∼22nm for Au film thicknesses of 4, 7, and 15nm, respectively, but roughly independent of Au grain size. These measurements are consistent with theoretical models that include multiple hot-electron scattering at interfaces and in the bulk of the metal film.
Spatio-Temporal Outdoor Lighting Aggregation on Image Sequences Using Transformer Networks (2022)

Abstract In this work, we focus on outdoor lighting estimation by aggregating individual noisy estimates from images, exploiting the rich image information from wide-angle cameras and/or temporal image sequences. Photographs inherently encode information about the lighting of the scene in the form of shading and shadows. Recovering the lighting is an inverse rendering problem and as that ill-posed. Recent research based on deep neural networks has shown promising results for estimating light from a single image, but with shortcomings in robustness. We tackle this problem by combining lighting estimates from several image views sampled in the angular and temporal domains of an image sequence. For this task, we introduce a transformer architecture that is trained in an end-2-end fashion without any statistical post-processing as required by previous work. Thereby, we propose a positional encoding that takes into account camera alignment and ego-motion estimation to globally register the individual estimates when computing attention between visual words. We show that our method leads to improved lighting estimation while requiring fewer hyperparameters compared to the state of the art.
Bioluminogenic Probe for Rapid, Ultrasensitive Detection of β-Lactam-Resistant Bacteria (2023)

Increasingly difficult-to-treat infections by antibiotic-resistant bacteria have become a major public health challenge. Rapid detection of common resistance mechanisms before empiric antibiotic usage is essential for optimizing therapeutic outcomes and containing further spread of resistance to antibiotics among other bacteria. Herein, we present a bioluminogenic probe, D-Bluco, for rapid detection of β-lactamase activity in viable pathogenic bacteria. D-Bluco is a pro-luciferin caged by a β-lactamase-responsive cephalosporin structure and further conjugated with a dabcyl quencher. The caging and quenching significantly decreased the initial background emission and increased the signal-to-background ratio by more than 1200-fold. D-Bluco was shown to detect a broad range of β-lactamases at the femtomolar level. An ultrasensitive RAPID bioluminescence assay using D-Bluco can detect 10<sup>2</sup> to 10<sup>3</sup> colony forming unit per milliliter (cfu/mL) of β-lactamase-producing <i>Enterobacterales</i> in urine samples within 30 min. The high sensitivity and rapid detection make the assay attractive for the use of point-of-care diagnostics for lactam-resistant pathogens.
Effects of the refractive index of the encapsulant on the light-extraction efficiency of light-emitting diodes (2011)

We investigate the effects of the refractive index of the encapsulant on the light-extraction efficiency (LEE) of light-emitting diodes (LEDs) for GaN LEDs (n ≈ 2.5) and AlGaInP LEDs (n ≈ 3.0). For non-absorbing rectangular parallelepiped LED chips, as the refractive index of the encapsulant increases, the LEE first increases quasi-linearly, then increases sub-linearly, and finally a saturation is reached. Furthermore, LEDs with a dual-layer graded-refractive-index (GRIN) encapsulant (n(encapsulant 1) = 1.57 and n(encapsulant 2) = 1.41) is fabricated through a two-step curing process. We demonstrate that such an LED further enhances the LEE by reducing Fresnel reflection loss at the encapsulant/air interface by 35% compared with an LED encapsulated with a single-layer encapsulant (n(encapsulant) = 1.57).
Detection for a Statistically Known (1996)

Detection for the statistically known channel (SKC) is aimed at obtaining good performance in situations where our statistical knowledge of a time-varying channel is good, and where other equallization/detection schemes are either too complex to implement, or their performance is limited due to the rapidity of channel fading, or where we are simply unable to perform channel estimation. By using a statistical characterization of the channel, we develop a new detector that performs maximum- likelihood sequence estimation (MLSE) (given the channel model) on blocks of N symbols. Both symbol-spaced and fractionally spaced samples are used, to obtain two different detectors, that are generalizations of those devised for optimal block schemes on nondispersive channels. The detector that uses fractionally spaced samples is shown to outperform the detector that uses symbol-spaced samples. The performance of both appears to approach that of the corresponding known channel (KC) detector as the blocklength increases. We also numerically evaluate the SKC detector performance under conditions where the channel parameters (statistics) are incorrectly estimated, and show that the fractionally spaced detector is fairly robust to modeling errors. Finally, we devise a sliding block algorithm, for use when transmitting more than N symbols.
ChemInform Abstract: Enantioselective Total Synthesis of Fumonisin B2. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A Co-design Approach for Hardware Optimizations in Multicore Architectures Using MCAPI (2015)

Current SoC platforms targeting high-performance with high power efficiency rely on replicating several processing cores while adding dedicated hardware units for specific tasks. However, programming such architectures demand a high effort when compared to homogeneous multiprocessors since there is no widely used standard for heterogeneous embedded systems. The use of standard application programming interfaces (APIs) increases the programmability but also costs performance/memory usage overheads. Providing mechanisms at the software level leveraging on dedicated hardware resources can help reducing that impact. To address this point, this work presents a co-design approach for improving programming based on a standard API deployed through a mix of hardware and software support for tasks synchronization. Results present a reduction of up to 88% in network traffic and processor active times during synchronization phases when compared to a pure software implementation.
Novel technology for microlenses for imaging applications (2018)

Microlenses are an important functional element of a modern imaging device. Typically, they are fabricated from organic materials on top of individual pixels. Though they are widely used, they do exhibit a number of limitations. These are, but not limited to, thermal stability, radiation sensitivity, outgassing properties, additional topography, and difficulty in manufacturing asymmetrical, noncircular microlens designs using conventional manufacturing techniques. In this paper, we present a novel approach for the fabrication of microlenses. We report on the design, manufacturing, and characterization of microlenses fabricated from classical dielectric materials used in the manufacturing of CMOS semiconductor devices. These microlenses rely on a Fresnel optical design, provide functionality similar to the classical microlenses, and do not suffer from their limitations. We subjected these microlenses to several environmental reliability stress conditions, including pressure, temperature, humidity, and their variation. Moreover, we test their sensitivity to gamma rays and protons.
Synthesis and some Physical Properties of trans-4–{β-(trans-4′-n-Alkylcyclohexyl)-1′} -Ethylcyclohexane-1 -Carboxylates (1984)

Abstract A series of trans-4–(β-(trans-4′-n-alkylcyclohexyl)-1′}-ethylcyclohexane-1-carboxylates, which show nematic phases, was prepared. Their transition temperatures and enthalpies were measured. Their bulk viscosities and birefringences were determined by extrapolation. The influence of terminal halogeno and alkyl groups on the N-I transition temperatures and the C-N transition enthalpies for the trans-4–(β-(trans-4′-n-alkylcy-clohexy1)-1′)-ethylcyclohexane-1-carboxylates is discussed and compared with the influence for the 1–(trans-4′-n-alkylcyclohexyl)-2–(4”-halobiphenyl-4′-yl)ethanes. The bulk viscosity as a function of the third power of the van der Waals radius of the halogeno group and the birefringence as a function of the van der Waals radius of the halogeno group for the 4-halophenyl trans-4′-{β-(trans-4”-n-propylcyclohexyl)-1”}-ethylcyclohexane-1′-carboxylates are discussed.
Virtual Resistor Active Damping with Selective Harmonics Control of LCL-Filtered VSCs (2021)

LCL filter is widely adopted for strict standard compliance of grid-tied voltage source converters (VSCs). The third order low-pass filtering provides great attenuation for the high frequency harmonics generated by the power electronics guaranteeing low output currents noise injection into the grid. A major concern of the implementation of the LCL-filter is to safeguard the system stability by providing effective damping of the filter resonances. Active damping methods are preferred because it does not result in substantial power losses as it would result by the utilization of passive damping circuits. Capacitor-current active damping (CCAD) technique can be effective while realizing only a proportional feedback. However, the suitable feedback gain for maintaining stability remains to be identified. Another control issue related to the grid-tied VSC is the harmonics compensation of the currents due to the grid voltage distortion. Therefore, this paper proposes an improved resonator with phase compensation to suppress the harmonics distortion while maintaining stability with properly design capacitor current feedback. The capacitor feedback gain for stability is analytically derived in this paper. The proposed control scheme is verified by both simulation and experimental results.
De novo mutations in inhibitors of Wnt, BMP, and Ras/ERK signaling pathways in non-syndromic midline craniosynostosis (2017)

Non-syndromic craniosynostosis (NSC) is a frequent congenital malformation in which one or more cranial sutures fuse prematurely. Mutations causing rare syndromic craniosynostoses in humans and engineered mouse models commonly increase signaling of the Wnt, bone morphogenetic protein (BMP), or Ras/ERK pathways, converging on shared nuclear targets that promote bone formation. In contrast, the genetics of NSC is largely unexplored. More than 95% of NSC is sporadic, suggesting a role for de novo mutations. Exome sequencing of 291 parent-offspring trios with midline NSC revealed 15 probands with heterozygous damaging de novo mutations in 12 negative regulators of Wnt, BMP, and Ras/ERK signaling (10.9-fold enrichment, <i>P</i> = 2.4 × 10<sup>-11</sup>). <i>SMAD6</i> had 4 de novo and 14 transmitted mutations; no other gene had more than 1. Four familial NSC kindreds had mutations in genes previously implicated in syndromic disease. Collectively, these mutations contribute to 10% of probands. Mutations are predominantly loss-of-function, implicating haploinsufficiency as a frequent mechanism. A common risk variant near <i>BMP2</i> increased the penetrance of <i>SMAD6</i> mutations and was overtransmitted to patients with de novo mutations in other genes in these pathways, supporting a frequent two-locus pathogenesis. These findings implicate new genes in NSC and demonstrate related pathophysiology of common non-syndromic and rare syndromic craniosynostoses. These findings have implications for diagnosis, risk of recurrence, and risk of adverse neurodevelopmental outcomes. Finally, the use of pathways identified in rare syndromic disease to find genes accounting for non-syndromic cases may prove broadly relevant to understanding other congenital disorders featuring high locus heterogeneity.
Kiviklusterihanke : Geofysikaalisten mittaustulosten ja louhinnan aikaisten havaintojen vertailu graniittilouhimolla (2013)

Osana Etelä-Karjalan kiviklusteri-hanketta tehtiin kivilouhimolla geofysikaalisia mittauksia,joiden tarkoituksena oli selvittää, pystytäänkö kallion halkeamia ja muita kiven ”vikoja” paikallistamaan mittausten avulla ennen louhintaa. Halkeamien ja muiden ei-toivottujen ominaisuuksien havaitseminen ennen louhintaa helpottaa louhinnan suunnittelua ja ennen louhimon avaamista tieto kiven laadusta auttaa toiminnan kannattavuuden arvioinnissa ja louhimon avaamispäätöksen tekemisessä.&#13;\n&#13;\nMittausmenetelminä olivat maatutkaus, magneettinen gradiometraus, sähkömagneettinen taajuusluotaus sekä rakojen havainnointi mittausten yhteydessä. Syvyysulottuvuutta mittauksilla oli noin 10 m. Lisäksi kaikkiin mittauksiin liittyi paikantamisen menettelyt. Tulkituista havainnoista koottiin malli, jossa havaitut epähomogeenisuudet on esitetty kolmiulotteisesti.&#13;\n&#13;\nTulkittua mallia verrattiin louhinnan aikana tehtyihin havaintoihin, joilla pyrittiin kartoittamaan louhinnan aikana esille tulevat raot, värivirheet ja muut viat, jotka&#13;\nhaittaavat myytäviksi tarkoitettujen kiviblokkien valmistusta. Kamin paloittelun seuranta tapahtui paikalla käynnein ja louhimon työnjohtajan tekemin havainnoin.&#13;\nPaikallakäyntien aikana pystyttiin seuraamaan uusien pintojen esille tuomia piirteitä vain kaatolohkareiden räjäytyksiin ja osittain kaatolohkareiden aihioiksi paloitteluun&#13;\nsaakka. Näin ollen kamin irrotusräjäytyksen jälkeen voitiin pääosin seurata kamin pitkittäissuunnassa esiin tulevia pintoja.&#13;\n&#13;\nKokonaisuutena todettujen rakojen ja piirteiden selitysastetta mallin kappaleilla voi pitää melko vaatimattomana. Seurannassa todetuista 43 raosta malli selittää 23 kpl eli 53.5 %. Toisaalta malli sisälsi vastaavilla pinnoilla paljon runsaammin niitä leikkaavia&#13;\npiirteitä, yhteensä 88 kpl. Näistä havainnot vastasivat 28 kpl eli selitysaste mallin kappaleille oli 31.8 %.&#13;\n&#13;\nVarsin yllättävänä voi pitää, etteivät magneettiset sinänsä voimakkaat ja jatkuvat anomaliat useinkaan selittyneet todetuilla raoilla. Sähkömagneettiset tulkinnat olivat jo&#13;\nvalmiiksi epävarmoja laitevian vuoksi. Ne kuitenkin sisällytettiin tulkintaan ja malliin, jotta voitiin tarkastella laitteen toimivuutta ja tulosten vastaavuutta eri menetelmien välillä.&#13;\n&#13;\nGeofysikaalisten mittausten perusteella tehdyt mallit eivät vastanneet kovin hyvin louhinnan aikana tehtyjä havaintoja. Projektissa valittiin käytettävät mittausmenetelmät ja siirryttiin suoraan mittausten tekemiseen. Mittausaikatauluun olisi pitänyt saada laiteteknistä testausta ennen varsinaisten mittausten tekemistä, ja selvitys kunkin&#13;\nmittausmenetelmän käytännön tarkkuudesta. Geofysiikan käyttö ja oikeiden tulkintojen tekeminen vaatii pitkäjänteisempää tutkimusta kuin mihin tässä projektissa oli&#13;\nmahdollisuuksia. Laitteita käyttävien henkilöiden ja tulkinnan tekijöiden pitää päästä vertaamaan mittaustuloksia ja todellisuutta pitemmällä aikavälillä ja kehittämään&#13;\nmenetelmiä ja tulosten tulkintaa saatujen kokemusten pohjalta.
Can NSEC5 be practical for DNSSEC deployments (2017)

NSEC5 is proposed modification to DNSSEC that simultaneously guarantees two security properties: (1) privacy against offline zone enumeration, and (2) integrity of zone contents, even if an adversary compromises the authoritative nameserver responsible for responding to DNS queries for the zone. This paper redesigns NSEC5 to make it both practical and performant. Our NSEC5 redesign features a new fast verifiable random function (VRF) based on elliptic curve cryptography (ECC), along with a cryptographic proof of its security. This VRF is also of independent interest, as it is being standardized by the IETF and being used by several other projects. We show how to integrate NSEC5 using our ECC-based VRF into the DNSSEC protocol, leveraging precomputation to improve performance and DNS protocol-level optimizations to shorten responses. Next, we present the first full-fledged implementation of NSEC5—extending widely-used DNS software to present a nameserver and recursive resolver that support NSEC5—and evaluate their performance under aggressive DNS query loads. Our performance results&#13;\nindicate that our redesigned NSEC5 can be viable even for high-throughput scenarios
<title>PHELIX: a petawatt high-energy laser for heavy ion experiments</title> (2001)

The unique combination of an intense heavy ion beam accelerator and a high energy laser opens the possibility of exploring new physics taking advantage of the synergy of both facilities. A variety of new fields can be addressed with this combination in plasma physics, atomic physics, nuclear- and astro-physics as well as material research. In addition, using CPA-technology, laser pulses with a pulse power of up to a petawatt opens the door to explore the regime of fully relativistic plasmas. Therefore the Gesellschaft fuer Schwerionenforschung is augmenting the current high intensity upgrade of the heavy ion accelerator facility with the construction of PHELIX. Designed with two pulse-generating front ends and send to multiple experimental areas PHELIX will serve as a highly versatile laser system for various applications. In this report, we present the design of the laser system and some key experiments that can be performed with this combination for the first time.