gebhart/patrepeval huggingface dataset:
The potential of VKORC1 polymorphisms in Mustelidae for evolving anticoagulant resistance through selection along the food chain (2019)

In response to strong selection, new mutations can arise quickly and sweep through populations, particularly, if survival and reproduction depend on certain allele copies for adaptation to rapidly changing environments, like resistance against deadly diseases or strong toxins. Since the 1950s, resistance to anticoagulant rodenticides in several rodents has emerged through single nucleotide mutations in the vitamin-K-epoxid-reductase-complex-subunit-1 (VKORC1) gene, often located in its exon 3. Detection of high prevalence and concentrations of anticoagulant rodenticides in non-target vertebrates, including carnivorous Mustelidae, let us assume that secondary exposure by feeding on poisoned prey may also cause selection along the food chain and we hypothesized that VKORC1-based resistance might also have evolved in rodents' predators. Using newly-developed mustelid-specific primers for direct sequencing of genomic DNA, we studied VKORC1-DNA-polymorphisms in 115 mustelids of five species (Martes martes, M. foina, Mustela nivalis, M. erminea, M. putorius), obtained from northern Denmark, yielding six sites with nonsynonymous and several synonymous amino acid polymorphisms in exon 3. Comparison of these VKORC1-genotypes with hepatic rodenticide residues (obtained by HPLC combined with fluorescence or mass spectrometry) in 83 individuals (except M. martes), using generalized linear models, suggested that anticoagulant levels depended on species and specific polymorphisms. Although most VKORC-1 polymorphisms may present standing genetic variation, some are situated in resistance-mediating membrane parts of the VKORC1-encoded protein, and might be a result of selection due to exposure to anticoagulant poisons. Our new molecular markers might allow detecting indirect effects of anticoagulant rodenticides on rodent predator populations in the future.
Analyzing initial geomorphologic processes and structures: An alternative remote sensing approach (2010)

The initial phase of the ecosystem development is usually characterized by overall imbalances and, thus, a huge dynamic of the ongoing processes. Especially the formation of surface structures due to erosion and sedimentation processes alters both the morphology and behaviour of the system. However, the quantification of these processes is not trivial. Some methods like classical terrestrial erosion measurement techniques might have undesirable effects on the ecosystem itself. Others, like laser scanning techniques do not influence the system but are very cost-intensive. An alternative method might be the photogrammetric analysis of aerial photographs. This technique allows for the calculation of precise digital elevation models not only with a high spatial but also temporal resolution. The amount of erosion and sedimentation processes can be quantified if digital elevation models calculated for different moments are compared.
Future microfluidic and nanofluidic modular platforms for nucleic acid liquid biopsy in precision medicine (2016)

Nucleic acid biomarkers have enormous potential in non-invasive diagnostics and disease management. In medical research and in the near future in the clinics, there is a great demand for accurate miRNA, mRNA, and ctDNA identification and profiling. They may lead to screening of early stage cancer that is not detectable by tissue biopsy or imaging. Moreover, because their cost is low and they are non-invasive, they can become a regular screening test during annual checkups or allow a dynamic treatment program that adjusts its drug and dosage frequently. We briefly review a few existing viral and endogenous RNA assays that have been approved by the Federal Drug Administration. These tests are based on the main nucleic acid detection technologies, namely, quantitative reverse transcription polymerase chain reaction (PCR), microarrays, and next-generation sequencing. Several of the challenges that these three technologies still face regarding the quantitative measurement of a panel of nucleic acids are outlined. Finally, we review a cluster of microfluidic technologies from our group with potential for point-of-care nucleic acid quantification without nucleic acid amplification, designed to overcome specific limitations of current technologies. We suggest that integration of these technologies in a modular design can offer a low-cost, robust, and yet sensitive/selective platform for a variety of precision medicine applications.
Microbe Profile: Campylobacter jejuni – survival instincts (2020)

<i>Campylobacter jejuni</i> is considered to be the most common bacterial cause of human gastroenteritis worldwide. <i>C. jejuni</i> can cause bloody diarrhoea, fever and abdominal pain in humans along with post-infectious sequelae such as Guillain-Barré syndrome (a paralytic autoimmune complication). <i>C. jejuni</i> infections can be fatal, particularly among young children. <i>C. jejuni</i> are distributed in most warm-blooded animals, and therefore the main route of transmission is generally foodborne, via the consumption and handling of meat products (particularly poultry). <i>C. jejuni</i> is microaerophilic and oxygen-sensitive, although it appears to be omnipresent in the environment, one of the many contradictions of <i>Campylobacter</i>.
Al-Catalyzed Enantioselective Alkylation of α-Ketoesters by Dialkylzinc Reagents. Enhancement of Enantioselectivity and Reactivity by an Achiral Lewis Base Additive (2005)

An Al-catalyzed enantioselective method for additions of Me(2)Zn and Et(2)Zn to alpha-ketoesters bearing aromatic, alkenyl, and alkyl substituents is disclosed. Transformations are promoted in the presence of a readily available amino acid-based ligand and afford the desired products in excellent yields and in up to 95% ee. Investigations described illustrate that the presence of a Lewis basic additive can lead to significant enhancements in efficiency and enantioselectivity. A mechanistic model that provides a rationale for such effects is provided.
Supplementary Tables S1-S2 from Integrative Genomic Analysis of Aneuploidy in Uveal Melanoma (2023)

Supplementary Tables S1-S2 from Integrative Genomic Analysis of Aneuploidy in Uveal Melanoma
Robust airborne navigation algorithms for SRGPS (2004)

Shipboard-relative GPS (SRGPS) is an architectural variant of the joint precision approach and landing system (JPALS) that provides high accuracy and high integrity DGPS navigation for automatic shipboard landings. This research is focused on the design of robust airborne algorithms for SRGPS terminal navigation. In this context, a processing methodology is defined to optimally combine the complementary benefits of geometry-free filtering and geometric redundancy. Specifically, when the aircraft is far from the ship (inside or outside the SRGPS service volume), geometry-free filtering is used for cycle estimation of widelane integers. For dual frequency implementations, the advantage of code/carrier divergence-free filtering prior to SRGPS service volume entry can be especially significant because long filter durations can be used. In this paper, the robust navigation architecture is detailed and its performance is evaluated relative to the navigation integrity requirements for shipboard landing of aircraft.
Laser ablation of dielectrics with pulse durations between 20 fs and 3 ps (1996)

Laser-induced ablation has been extended down to a pulse duration of 20 fs generated by a Ti sapphire laser system at a wavelength of 780 nm. Barium aluminum borosilicate glass with an extremely high glass transformation temperature (∼600 °C) served as target material. The most significant observation was a substantial decrease of the ablation threshold fluence at pulse durations below 100 fs. All results indicate a dominant role of multiphoton absorption in addition to collisional ionization in this time domain.
Potent Oxazolidinone Antibacterials with Heteroaromatic C-Ring Substructure (2013)

Novel oxazolidinone analogues bearing a condensed heteroaromatic ring as the C-ring substructure were synthesized as candidate antibacterial agents. Analogues 16 and 21 bearing imidazo[1,2-a]pyridine and 18 and 23 bearing [1,2,4]triazolo[1,5-a]pyridine as the C-ring had excellent in vitro antibacterial activities against methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecalis (VRE), and penicillin-resistant Streptococcus pneumoniae (PRSP). They also showed promising therapeutic effects in a mouse model of lethal infection. Preliminary safety data (inhibitory effects on cytochrome P450 isoforms and monoamine oxidases) were satisfactory. Further evaluation of 18 and 23 is ongoing.
Detection of c- abl Tyrosine Kinase Activity In Vitro Permits Direct Comparison of Normal and Altered abl Gene Products (1985)

The v-abl transforming protein P160v-abl and the P210c-abl gene product of the translocated c-abl gene in Philadelphia chromosome-positive chronic myelogenous leukemia cells have tyrosine-specific protein kinase activity. Under similar assay conditions the normal c-abl gene products, murine P150c-abl and human P145c-abl, lacked detectable kinase activity. Reaction conditions were modified to identify conditions which would permit the detection of c-abl tyrosine kinase activity. It was found that the Formalin-fixed Staphylococcus aureus formerly used for immunoprecipitation inhibits in vitro abl kinase activity. In addition, the sodium dodecyl sulfate and deoxycholate detergents formerly used in the cell lysis buffer were found to decrease recovered abl kinase activity. The discovery of assay conditions for c-abl kinase activity now makes it possible to compare P150c-abl and P145c-abl kinase activity with the altered abl proteins P160v-abl and P210c-abl. Although all of the abl proteins have in vitro tyrosine kinase activity, they differ in the way they utilize themselves as substrates in vitro. Comparison of in vitro and in vivo tyrosine phosphorylation sites of the abl proteins suggests that they function differently in vivo. The development of c-abl kinase assay conditions should be useful in elucidating c-abl function.
Efficient cross-talk reduction of nanophotonic circuits enabled by periodic silicon strip arrays (2017)

We develop a simple and efficient crosstalk reduction approach for Si-based nanophotonic circuits by introducing a periodic array of Si strips between adjacent waveguides. Studies indicate that the coupling length can be extended by more than two orders of magnitude for a waveguide pair with an edge-to-edge distance of ~λ/3. Our approach offers a feasible route toward photonic integrated circuits with an ultra-high packing density.
Impact of PtRu Anode Catalyst Degradation on DMFC MEA Performance (2008)

This paper reports an 'MEA based' accelerated ageing test designed primarily to investigate stability of anode catalysts for DMFCs. The effect of potential cycling on the anode with increasing number of cycles is investigated. Methanol stripping voltammetry is used to characterize changes at both the anode and cathode catalysts and the changes observed are related to quantitative changes in performance of the MEA polarization data. Changes in catalyst morphology and surface composition are characterized by TEM. In particular, comparisons between unsupported PtRu ('black') and carbon supported PtRu catalysts are made.
Perception in Hand-Worn Haptics: Placement, Simultaneous Stimuli, and Vibration Motor Comparisons (2016)

Glove-based tactile interfaces are used for augmented reality, rehabilitation, teaching, and consumer electronics control. Yet questions remain regarding perception of tactile stimuli on the hands. In an effort to inform the design of such tactile interfaces, we investigate participants' abilities to sense vibration on the hands. First, we examine the effect of stimulus location on recognition accuracy. Ventral (palm-side) placement on the fingers is critical: accuracy increases with proximity to the palm, linearly, on all fingers. Second, we study perception of multiple simultaneous vibrations on the fingers. Recognition degrades with increasing number of simultaneous tactile stimuli and no subitizing is found. Error is &gt;60-80\\% for more than two simultaneous stimuli points. Our third study compares the perception of Eccentric Rotating Mass (ERM) and Linear Resonant Actuator (LRA) vibration motors. Recognition accuracy was less using LRA motors, especially in placements on the palm side of the fingers (-20.3% versus -10.1% for ERM). Correct recognition of chords was also less or comparable using LRA motors, suggesting that the ERM motor is preferable.
WAMS BASEDFLOW TRANSFERRING INDENTIFICATION ALGORITHM AND ITSIMPLEMENTATION (2006)

When relays tripa faulted lineinpower system, theflowonthefaulted line willbetransferred to theotherlines. Thoselines mightbeoverloaded andthen cascading tripped bythebackuprelays, whichworsenthe systemstate andevencauseblackout. Generally, these kindofcascading trips aretheorigins ofalotofwell- knownblackouts. Inthis paper, byanalyzing thedefects of traditional backupprotections, a newwideareabackup protection schemebasedon WAMS ispresented to identify flowtransferring. A new conceptof Flow Transferring Relativity Factor(FTRF)isproposed to estimate theflowdistribution afterflowtransferring occurs; andthemethodofcalculating FTRF matrixon- line isalsodeduced. Thesimulation of10-unit and39-bus NewEngland network showsthattheproposed widearea backupprotection schemecanidentify flowtransferring successfully andhencebe superior tothetraditional backupprotection.
Association of serum monomeric periostin level with outcomes of acute exacerbation of idiopathic pulmonary fibrosis and fibrosing nonspecific interstitial pneumonia (2021)

Serial change in serum M-PN level may be a prognostic indicator of AE-FIP.
Thermally assisted recording beyond traditional limits (2004)

This work demonstrates that current magnetic storage density limitations due to superparamagnetic effects can be overcome by thermally assisted writing. Specifically, we write magnetization patterns on thin magnetic films that correspond to storage densities of ∼400 Gbit/in.2. Simple thermal diffusion considerations predict potential storage densities of &amp;gt;1 Tbit/in.2 accompanied by recording speeds of &amp;gt;1 GHz.
Slow-light enhancement of radiation pressure in an omnidirectional-reflector waveguide (2004)

We study the radiation pressure on the surface of a waveguide formed by omnidirectionally reflecting mirrors. In the absence of losses, the pressure goes to infinity as the distance between the mirrors is reduced to the cutoff separation of the waveguide mode. This divergence at constant power input is due to the reduction of the modal group velocity to zero, which results in the magnification of the electromagnetic field. Our structure suggests a promising alternative, microscale system for observing the variety of classical and quantum-optical effects associated with radiation pressure in Fabry–Perot cavities.
Zinc Finger Database (ZiFDB) v2.0: a comprehensive database of C2H2 zinc fingers and engineered zinc finger arrays (2012)

ZiFDB (Zinc Finger Database, http://zifdb.msi.umn.edu) is a web-accessible database that houses information on individual C(2)H(2) zinc fingers (ZFs) and engineered zinc finger arrays (ZFAs). ZiFDB serves as a resource for biologists interested in engineering ZFAs for use as sequence-specific DNA-binding reagents. Here, we describe four new features of ZiFDB: (i) the database allows users to input new ZFs and ZFAs; (ii) a shadow database temporarily stores user-submitted data, pending approval by the database curator and subsequent loading into the persistent database; (iii) ZiFDB contains 181 Context-Dependent Assembly (CoDA) ZFAs, which were generated by this newly described ZFA engineering platform; and (iv) the database also now contains 319 F1F2 CoDA units and 334 F2F3 CoDA units that can be used to construct CoDA arrays. In total, the new release of ZiFDB contains 1226 ZFs and 1123 ZFAs.
c-Myc Immunohistochemistry in Diffuse Large B Cell Lymphoma (2014)

Diffuse large B cell lymphoma is a collection of different biologic entities with a common appearance but different clinical behaviors. The MYC oncogene is mutated in a subset of diffuse large B cell lymphoma and is also mutated in related entities such as Burkitt lymphoma. Recently, an antibody to the c-Myc oncoprotein has become available for immunohistochemistry, raising the possibility of a rapid, reproducible and inexpensive measure of MYC abnormality. Initial retrospective studies of these lymphomas suggest that the c-Myc status is clinically important for diagnosis and prognosis, particularly when used in conjunction with BCL2 immunohistochemistry. It is possible that therapy will be modified based in part on c-Myc status, once the appropriate prospective studies have been performed.
The PKN1- TRAF1 signaling axis as a potential new target for chronic lymphocytic leukemia (2021)

Abstract TRAF1 is a pro-survival adaptor molecule in TNFR superfamily (TNFRSF) signaling. TRAF1 is overexpressed in many B cell cancers including refractory chronic lymphocytic leukemia (CLL). Little has been done to assess the role of TRAF1 in human cancer. Here we show that the protein kinase C related kinase Protein Kinase N1 (PKN1) is required to protect TRAF1 from cIAP-mediated degradation during constitutive CD40 signaling in lymphoma. We show that the active phospho-Thr774 form of PKN1 is constitutively expressed in CLL but minimally detected in unstimulated healthy donor B cells. Through a screen of 700 kinase inhibitors, we identified two inhibitors, OTSSP167 and XL-228, that inhibited PKN1 in the nanomolar range and induced dose-dependent loss of TRAF1 in RAJI cells. OTSSP167 and XL-228 treatment of primary patient CLL samples led to a reduction in TRAF1, pNF-κB p65, pS6, pERK, Mcl-1 and Bcl-2 proteins, and induction of activated caspase-3. OTSSP167 synergized with venetoclax in inducing CLL death, correlating with loss of TRAF1, Mcl-1 and Bcl-2. Although correlative, these findings suggest the PKN1-TRAF1 signaling axis as a potential new target for CLL. These findings also suggest OTSSP167 and venetoclax as a combination treatment for TRAF1 high CLL.
Supplementary Table 1 from The miR-17/92 Polycistron Is Up-regulated in Sonic Hedgehog–Driven Medulloblastomas and Induced by N-myc in Sonic Hedgehog–Treated Cerebellar Neural Precursors (2023)

Supplementary Table 1 from The miR-17/92 Polycistron Is Up-regulated in Sonic Hedgehog–Driven Medulloblastomas and Induced by N-myc in Sonic Hedgehog–Treated Cerebellar Neural Precursors
Privacy-Preserving Payment Splitting (2020)

Abstract Widely used payment splitting apps allow members of a group to keep track of debts between members by sending charges for expenses paid by one member on behalf of others. While offering a great deal of convenience, these apps gain access to sensitive data on users’ financial transactions. In this paper, we present a payment splitting app that hides all transaction data within a group from the service provider, provides privacy protections between users in a group, and provides integrity against malicious users or even a malicious server. The core protocol proceeds in a series of rounds in which users either submit real data or cover traffic, and the server blindly updates balances, informs users of charges, and computes integrity checks on user-submitted data. Our protocol requires no cryptographic operations on the server, and after a group’s initial setup, the only cryptographic tool users need is AES. We implement the payment splitting protocol as an Android app and the accompanying server. We find that, for realistic group sizes, it requires fewer than 50 milliseconds per round of computation on a user’s phone and the server requires fewer than 300 micro seconds per round for each group, meaning that our protocol enjoys excellent performance and scalability properties.
Extractant Forced-Circulation Three-Phase Extraction for the Preconcentration of Parts-per-Billion (Ppb)-Level Cadmium(II) from Natural Waters (2020)

An extractant forced-circulation three-phase extraction (EC-TPE) device based on extraction-stripping coupling was developed for the preconcentration of Cd2+ in environmental samples. In this three-phase extraction (W1/O↔O/W2) system, Cd2+ in the sample solution (W1) was fully extracted into the stripping phase (W2) by the circular flow of an organic phase (O↔O). The extraction yield (EY) and enrichment factor (EF) reached almost 100% and 100, respectively, under the following operating conditions: 0.1 M HNO3, 2 mL/L di(2-ethylhexyl)phosphoric acid (P204), circulation flow rate of 32 mL/min, circulation time of 45 min and stirring speed of 400 rpm. An extraction yield of more than 98.5% was still achieved after reusing the organic phase eight times. Two theoretical formulas were established for predicting the EY and EF. Thereafter, EC-TPE was applied in the preconcentration of ppb-level Cd2+ for flame atomic absorption spectrophotometer assay with a detection limit of 0.17 μg/L. Addition/recovery tests for Cd2+ were carried out with recoveries exceeding 98%, and three environmental water samples were accurately analyzed. Finally, application of the EC-TPE device was extended to a different extraction system and other metal ions: Zn2+, Cu2+, Ni2+, and Co2+. The EC-TPE device is easily established utilizing common laboratory glassware, and the enrichment operation efficiency can be conveniently improved by using more than one device simultaneously.