gebhart/patrepeval huggingface dataset:
Glyoxylic acid promotes poly(ADP-ribosyl)ation of nuclear proteins in K562 cells cultured at limiting dilution. (1990)

Addition of glyoxylic acid to the culture medium allows survival and proliferation of K562 human erythroleukemic cells cultured at low population density in the absence of serum. Concomitantly, glyoxylic acid induces a remarkable increase in nuclear poly(ADP-ribose) content, as compared to control cells cultured without addition of glyoxylate. The latter effect is reversed by addition of micromolar concentrations of benzamide to the cultures. As glyoxylic acid is metabolized through NADH-dependent reduction to glycolic acid only, the observed effects on cell growth and on nuclear poly(ADP-ribose) content seem to be mediated by an increased cellular ability to oxidize NADH.
Effects of feeding spray-dried plasma to broiler breeders and their progeny on broiler performance under stressful rearing conditions of coccidial challenge and heat stress (2023)

A total of 216 Cobb 500 broiler breeder hens were randomly distributed across 2 dietary treatments with 0 or 1% spray-dried plasma (SDP) resulting in 27 replications/treatment and 4 birds/replication. In addition, 36 roosters were divided between the same treatments and housed, in individual pens, being each bird considered a replicate. Experimental diets were fed from 26 wk until 65 wk of age. At 29, 45, and 63 wk of age, broiler breeder hens were inseminated, and eggs were incubated. Three progeny studies were performed and hatched birds were allocated in a randomized 2 × 2 factorial design (maternal diet: with or without inclusion of 1% SDP × progeny diet: with or without the inclusion of 2% SDP from 1 to 7 d of age). After 7 d of age, all birds received the same diet until 42 d. In all trials, birds were challenged with coccidiosis vaccine at 7 d of age. Furthermore, in the second experiment, heat stress was also included for 6 h a day during the whole trial. At 42-days posthatch in the first experiment, greater FI, BW, and BWG in chicks hatched from breeders fed 1% dietary SDP was observed. This effect did not extend to the other hatches. In the second trial, a decreased FCR in broilers fed the control diet from breeder hens fed 1 % of SDP was observed, as well as an interaction between the SDP groups, since broilers supplemented with SDP and originated from breeders fed SDP showed higher BW and BWG in comparison to other groups at 42 d. In the third trial, contrary to what was observed in the first study, SDP supplementation did not affect any of the performance indexes. In the 3 studies, no differences were found in carcass characteristics. SDP did not affect hen BW, egg production, fertility, or hatch of fertile. These results suggest that providing dietary SDP to broilers has some beneficial effects on broiler chickens.
Variability in arabinoxylan, xylanase activity, and xylanase inhibitor levels in hard spring wheat (2012)

Arabinoxylans (AX), xylanase, and xylanase inhibitors have an important role in many cereal food processing applications.The effect of growing location (L), genotype (G), and their interactions (L*G) on AX, apparent xylanase and apparent xylanase inhibition activities of Triticum aestivum xylanase inhibitor (TAXI) and xylanases inhibiting protein (XIP) of wheat was studied using six hard red spring wheat and six hard white spring wheat genotypes.Total AX content was largely dependent on L*G.In bran, xylanase activity, 25% of the variability could be attributed to L*G interaction.Genotype contributed 72% to the variability in TAXI activity indicating TAXI activity in wheat bran is largely under genetic control.The bran TAXI level and XIP level varied by a factor of 700 and 3000, respectively, among genotypes.These results enable the industry to choose between different wheat varieties with varying xylanase activities to complement its intended use.
Inverse Procedural Modeling of Branching Structures by Inferring L-Systems (2020)

We introduce an inverse procedural modeling approach that learns L-system representations of pixel images with branching structures. Our fully automatic model generates a compact set of textual rewriting rules that describe the input. We use deep learning to discover atomic structures such as line segments or branchings. Orientation and scaling of these structures are determined and the detected structures are combined into a tree. The initial representation is analyzed, and repeating parts are encoded into a small grammar by using greedy optimization while the user can control the size of the detected rules. The output is an L-system that represents the input image as a simple text and a set of terminal symbols. We apply our approach to a variety of examples, demonstrate its robustness against noise and blur, and we show that it can detect user sketches and complex input structures.
Secondary-electron signal level measurements of self-assembled monolayers for spatial-phase-locked electron-beam lithography (2011)

The secondary-electron signal levels of eight thiophenol-based self-assembled monolayers (SAMs) on gold (Au) are measured and compared against the signal level from bare gold between energies 1 and 2 keV. To enable accurate comparison, scanning electron micrographs of SAMs are taken with a Faraday cup and a reference sample. Most SAMs-on-gold produce a lower signal level than that from bare gold, with the exception of 3-methylthiophenol. Highest occupied molecular orbital and lowest unoccupied molecular orbital levels of the thiophenol derivatives are calculated and compared against the signal levels. Signal levels from bis[3-(triethoxysilyl)propyl]tetrasulfide, (4-chlorophenyl)-triethoxysilane, and amino-propyl-triethoxy-silane on titanium (Ti) and aluminum (Al) are also measured. All three SAMs on aluminum have lower signal levels than bare Al but this effect is reversed for the case of Ti, where SAMs deposited on Ti result in a higher signal level. A hybrid Ti/Al fiducial grid is fabricated and the point-spread function at 2 keV in the underlying resist is investigated.
Sequences of V kappa L subgroup light chains in Fanconi's syndrome. Light chain V region gene usage restriction and peculiarities in myeloma-associated Fanconi's syndrome (1995)

Certain monoclonal Ig light chains (LC) are responsible for marked disturbances of proximal tubule cell functions (Fanconi's syndrome, FS). In patients with FS, intracellular crystal-like inclusions containing LC determinants are commonly found in plasma cells, macrophages, and renal tubular cells. In an attempt at understanding the pathogenesis of myeloma-associated FS, we recently determined the first complete primary sequence of a kappa-LC (CHEB) responsible for the disease. We now report on the primary structure of three other kappa-LC of the V kappa l variability subgroup associated with FS (TRE, TRO, and DEL). After PCR amplification, cDNA encoding these LC were sequenced. CHEB, TRE, and TRO LC genes were found to be highly homologous to the same germline gene O2/O12. These patients had numerous intracellular crystals, whereas the fourth patient, DEL, had no detectable crystals. The LC from the latter patient was homologous to another germline gene, O8/O18. Comparison of these LC sequences to previously reported LC of the V kappa l subgroup allowed identification of a number of unusual amino acid substitutions in the V region that had rarely or never been previously described at the corresponding positions. Some of these unusual substitutions affect highly conserved amino acids located either in an external loop (residue 30) or in inner (residues 48 and 55) and outer (positions 63 and 72) beta-sheets that may be important for the structure and binding properties of the kappa-chains. These and several other substitutions, some of them shared with amyloidogenic kappa-LC, could induce conformational alterations and represent a determinant pathogenic factor.
A reconfigurable photonic bandpass RF filter employing a semiconductor optical amplifier and an opto-VLSI processor (2006)

In this paper, a reconfigurable photonic bandpass RF filter employing a semiconductor optical amplifier (SOA) and an Opto-VLSI processor is proposed where a high coherent RF modulated laser carrier is fed into the SOA and through cross-gain modulation, a low coherence RF-modulated amplified spontaneous emission (ASE) can be generated. By spectrally slicing the ASE with an optical comb filter, RF-modulated wavebands of different centre wavelengths are generated. These RF-modulated wavebands are then processed by an Opto-VLSI processor which arbitrarily shapes the intensity profile of the wavebands. A high-dispersion optical fibre introduces linear true-time delays between the different wavebands so that after photodetection a photonic bandpass RF filter with multiple taps is realised. The proof-of- concept of the photonic bandpass filter is experimentally demonstrated, and results show that the filter can operate at 3.6 GHz with more than 25 dB rejection and its working frequency can be tuned by reconfigurable holograms generated by the Opto-VLSI processor. The filter can work with the laser carrier wavelength in the range of 1523nm to 1566nm without any optical coherence noises.
Distributed Denial-of-Service Open Threat Signaling (DOTS) Signal Channel Specification (2020)

This document specifies the DOTS signal channel, a protocol for
signaling the need for protection against Distributed Denial-of-
Service (DDoS) attacks to a server capable of enabling network traffic
mitigation on behalf of the requesting client. A companion document
defines the DOTS data channel, a separate reliable communication layer
for DOTS management and configuration purposes. Editorial Note (To be
removed by Editor) Please update these statements within the
document with the number to be assigned to this document: o This
version of this YANG module is part of XXXX; o RFC XXXX:
Distributed Denial-of-Service Open Threat Signaling (DOTS) Signal
Channel Specification; o [RFCXXXX] | o reference: XXXX
Please update this statement with the number to be assigned to the
following documents: o RFC YYYY: Distributed Denial-of-Service Open
Threat Signaling (DOTS) Data Channel Specification (used to be I-D
.ietf-dots-data- channel) Please update TBD/TBD1/TBD2 statements with
the assignments made by IANA to DOTS Signal Channel Protocol. Also,
please update the revision date of the YANG modules.
Digital Twin Aided IC Packaging Structure Analysis for High-quality Sample Preparation (2021)

Increased outsourcing of Integrated Circuit (IC) design and fabrication combined with malicious hardware security threats such as contactless optical probing have greatly decreased an attacker’s difficulty in reverse engineering or maliciously modifying a given circuit. This has become a significant concern for the safety and security of the semiconductor industry. Physical inspection techniques have been used to validate the IC hardware integrity and detect security threats to address these concerns. However, most physical inspection methods for ICs rely upon removing unwanted epoxy packaging material without damaging the device under test (DUT). Therefore, the precise removal of the IC packaging guided by knowledge of the packaging structure is very important for efficiency and accuracy in this process. Currently, IC structure analysis depends on using high-resolution X-ray computed tomography (CT), which is time-consuming and lacks the spatial resolution necessary for characterizing advanced heterogeneous packages. For hardware assurance purposes, the entire volume of a device must be analyzed with high efficacy. Additionally, various packaging and the recently adopted 2.5D and 3D advanced packages bring more challenges to meet assurance requirements. Hybrid metrology, which is the combined use of inspection methods for characterization, has the potential to address the inspection challenges for advanced packaging. In this paper, a novel hybridized inspection method utilizing nondestructive THz time-domain spectrum (THz-TDS) and X-ray CT of the IC package is used to create a digital twin (DT) of the sample. The combined characterization can be leveraged to improve the efficiency and accuracy for high quality sample preparation. Hybrid inspection paired with automated sample preparation can reduce the time and operator input needed for complete verification of a large volume of samples. In this paper, the method of generating a digital twin of the IC internal regions of interest (ROI) will be introduced. Analysis of the generated digital twin is used to optimize the material removal necessary for IC verification without damaging the ROI. This inspection and removal methodology can be automated using boundary conditions from the design information of the IC package. Hybrid inspection provides the high spatial resolution thickness and geometry information for generating an automated material removal routine. This provides access to the sample’s ROI for further FIB plasma delayering and SEM verification.
Cytotoxicity of CD56bright NK Cells towards Autologous Activated CD4+ T Cells Is Mediated through NKG2D, LFA-1 and TRAIL and Dampened via CD94/NKG2A (2012)

In mouse models of chronic inflammatory diseases, Natural Killer (NK) cells can play an immunoregulatory role by eliminating chronically activated leukocytes. Indirect evidence suggests that NK cells may also be immunoregulatory in humans. Two subsets of human NK cells can be phenotypically distinguished as CD16(+)CD56(dim) and CD16(dim/-)CD56(bright). An expansion in the CD56(bright) NK cell subset has been associated with clinical responses to therapy in various autoimmune diseases, suggesting an immunoregulatory role for this subset in vivo. Here we compared the regulation of activated human CD4(+) T cells by CD56(dim) and CD56(bright) autologous NK cells in vitro. Both subsets efficiently killed activated, but not resting, CD4(+) T cells. The activating receptor NKG2D, as well as the integrin LFA-1 and the TRAIL pathway, played important roles in this process. Degranulation by NK cells towards activated CD4(+) T cells was enhanced by IL-2, IL-15, IL-12+IL-18 and IFN-α. Interestingly, IL-7 and IL-21 stimulated degranulation by CD56(bright) NK cells but not by CD56(dim) NK cells. NK cell killing of activated CD4(+) T cells was suppressed by HLA-E on CD4(+) T cells, as blocking the interaction between HLA-E and the inhibitory CD94/NKG2A NK cell receptor enhanced NK cell degranulation. This study provides new insight into CD56(dim) and CD56(bright) NK cell-mediated elimination of activated autologous CD4(+) T cells, which potentially may provide an opportunity for therapeutic treatment of chronic inflammation.
Automorphisms of one-relator groups (1999)

It is a well known fact that every group G has a presentation of the form G=F/R, where F is a free group and R the kernel of the natural epimorphism from F onto G. Driven by the desire to obtain a similar presentation of the group of automorphisms Aut (G), we consider the subgroup Stab (R) ⊆ Aut (F) of those automorphisms of F that stabilize R and ask whether the natural homomorphism Stab (R) → Aut (G) is onto; if it is, we can try to determine its kernel.Both parts of this task are usually quite hard. The former part received considerable attention in the past, whereas the more difficult part (determining the kernel) seemed unapproachable. Here we approach this problem for a class of one-relator groups with a special kind of small cancellation condition. Then, we address a somewhat easier case of 2-generator (not necessarily one-relator) groups and determine the kernel of the above-mentioned homomorphism for a rather general class of those groups.
Lithotrophic iron-oxidizing bacteria produce organic stalks to control mineral growth: implications for biosignature formation (2010)

Neutrophilic Fe-oxidizing bacteria (FeOB) are often identified by their distinctive morphologies, such as the extracellular twisted ribbon-like stalks formed by Gallionella ferruginea or Mariprofundus ferrooxydans. Similar filaments preserved in silica are often identified as FeOB fossils in rocks. Although it is assumed that twisted iron stalks are indicative of FeOB, the stalk's metabolic role has not been established. To this end, we studied the marine FeOB M. ferrooxydans by light, X-ray and electron microscopy. Using time-lapse light microscopy, we observed cells excreting stalks during growth (averaging 2.2 μm h(-1)). Scanning transmission X-ray microscopy and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy show that stalks are Fe(III)-rich, whereas cells are low in Fe. Transmission electron microscopy reveals that stalks are composed of several fibrils, which contain few-nanometer-sized iron oxyhydroxide crystals. Lepidocrocite crystals that nucleated on the fibril surface are much larger (∼100 nm), suggesting that mineral growth within fibrils is retarded, relative to sites surrounding fibrils. C and N 1s NEXAFS spectroscopy and fluorescence probing show that stalks primarily contain carboxyl-rich polysaccharides. On the basis of these results, we suggest a physiological model for Fe oxidation in which cells excrete oxidized Fe bound to organic polymers. These organic molecules retard mineral growth, preventing cell encrustation. This model describes an essential role for stalk formation in FeOB growth. We suggest that stalk-like morphologies observed in modern and ancient samples may be correlated confidently with the Fe-oxidizing metabolism as a robust biosignature.
Vulnerability of invasive glioblastoma cells to lysosomal membrane destabilization (2019)

The current clinical care of glioblastomas leaves behind invasive, radio- and chemo-resistant cells. We recently identified mammary-derived growth inhibitor (MDGI/<i>FABP3</i>) as a biomarker for invasive gliomas. Here, we demonstrate a novel function for MDGI in the maintenance of lysosomal membrane integrity, thus rendering invasive glioma cells unexpectedly vulnerable to lysosomal membrane destabilization. MDGI silencing impaired trafficking of polyunsaturated fatty acids into cells resulting in significant alterations in the lipid composition of lysosomal membranes, and subsequent death of the patient-derived glioma cells via lysosomal membrane permeabilization (LMP). In a preclinical model, treatment of glioma-bearing mice with an antihistaminergic LMP-inducing drug efficiently eradicated invasive glioma cells and secondary tumours within the brain. This unexpected fragility of the aggressive infiltrating cells to LMP provides new opportunities for clinical interventions, such as re-positioning of an established antihistamine drug, to eradicate the inoperable, invasive, and chemo-resistant glioma cells from sustaining disease progression and recurrence.
A novel unsupervised spike sorting algorithm for intracranial EEG (2011)

This paper presents a novel, unsupervised spike classification algorithm for intracranial EEG. The method combines template matching and principal component analysis (PCA) for building a dynamic patient-specific codebook without a priori knowledge of the spike waveforms. The problem of misclassification due to overlapping classes is resolved by identifying similar classes in the codebook using hierarchical clustering. Cluster quality is visually assessed by projecting inter- and intra-clusters onto a 3D plot. Intracranial EEG from 5 patients was utilized to optimize the algorithm. The resulting codebook retains 82.1% of the detected spikes in non-overlapping and disjoint clusters. Initial results suggest a definite role of this method for both rapid review and quantitation of interictal spikes that could enhance both clinical treatment and research studies on epileptic patients.
Adaptive four-level modeling of laser cooling of solids (2021)

Laser cooling of rare-earth doped solids has been demonstrated across a wide range of material platforms, inspiring the development of simple phenomenological models such as the four-level model to elucidate the universal properties of laser cooling under various operating conditions. However, these models usually require the input of full absorption spectra that must be provided experimentally or by additional complicated atomic modeling. In this Letter, we propose that a four-level model, when extended to admit effective energy levels adaptive to the pumping photon energy, can accurately predict the cooling efficiency as a function of temperature and pumping frequency using only few inputs such as the absorption coefficient measured at a single frequency and temperature. Our model exploits the quasi-equilibrium properties of the excitation of rare-earth ions for the determination of the effective four energy levels. The model is validated against published experimental results for a span of materials including ytterbium/thulium-doped glass and crystals. With the verified model, we derive explicit expressions for the optimal frequency and the operating bandwidth of pumping lasers. Our model significantly simplifies the modeling process of laser cooling and is expected to stimulate further development of optical refrigeration.
ChemInform Abstract: Transformations of Chloroarenes, Catalyzed by Transition‐Metal Complexes (1994)

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.
Correlation between CT numbers and tissue parameters needed for Monte Carlo simulations of clinical dose distributions (2000)

We describe a new method to convert CT numbers into mass density and elemental weights of tissues required as input for dose calculations with Monte Carlo codes such as EGS4. As a first step, we calculate the CT numbers for 71 human tissues. To reduce the effort for the necessary fits of the CT numbers to mass density and elemental weights, we establish four sections on the CT number scale, each confined by selected tissues. Within each section, the mass density and elemental weights of the selected tissues are interpolated. For this purpose, functional relationships between the CT number and each of the tissue parameters, valid for media which are composed of only two components in varying proportions, are derived. Compared with conventional data fits, no loss of accuracy is accepted when using the interpolation functions. Assuming plausible values for the deviations of calculated and measured CT numbers, the mass density can be determined with an accuracy better than 0.04 g cm(-3). The weights of phosphorus and calcium can be determined with maximum uncertainties of 1 or 2.3 percentage points (pp) respectively. Similar values can be achieved for hydrogen (0.8 pp) and nitrogen (3 pp). For carbon and oxygen weights, errors up to 14 pp can occur. The influence of the elemental weights on the results of Monte Carlo dose calculations is investigated and discussed.
STUDY FOR A COMPREHENSIVE BRIDGE MANAGEMENT SYSTEM FOR TEXAS. FINAL REPORT. REVISED JULY 1991 (1991)

This report covers a two-year study of the feasibility and development of specific recommendations for a comprehensive bridge management system (BMS) for the Texas State Department of Highways and Public Transportation. The study identified the problems which could advantageously be addressed by a BMS and recommends a scope for a proposed BMS which is believed to be appropriate for application at district and state level. The study also included review of BMSs proposed, developed, and used in other states and reviews of theory and technology relevant to the sub-problems comprising the overall bridge management problem. Finally, the study addresses the problem of identifying the data required for the application of a BMS in Texas.