gebhart/patrepeval huggingface dataset:
Tensor-cell2cell v2 unravels coordinated dynamics of protein- and metabolite-mediated cell-cell communication (2022)

Cell-cell communication dynamically changes across time while involving diverse cell populations and ligand types such as proteins and metabolites. While single-cell transcriptomics enables its inference, existing tools typically analyze ligand types separately and overlook their coordinated activity. Here, we present Tensor-cell2cell v2, a computational tool that can jointly analyze protein- and metabolite-mediated communication over time using coupled tensor component analysis, while preserving each modality of inferred communication scores independently, as well as their data structures and distributions. Applied to brain organoid development, Tensor-cell2cell v2 uncovers dynamic, coordinated communication programs involving key proteins and metabolites across relevant cell types across specific time points.
Functional importance of a conserved sequence motif in FhaC, a prototypic member of the TpsB/Omp85 superfamily (2010)

In Gram-negative bacteria, the two-partner secretion pathway mediates the secretion of TpsA proteins with various functions. TpsB transporters specifically recognize their TpsA partners in the periplasm and mediate their transport through a hydrophilic channel. The filamentous haemagglutinin adhesin (FHA)/FhaC pair represents a model two-partner secretion system, with the structure of the TpsB transporter FhaC providing the bases to decipher the mechanism of action of these proteins. FhaC is composed of a β-barrel preceded by two periplasmic polypeptide-transport-associated (POTRA) domains in tandem. The barrel is occluded by an N-terminal helix and an extracellular loop, L6, folded back into the FhaC channel. In this article, we describe a functionally important motif of FhaC. The VRGY tetrad is highly conserved in the TpsB family and, in FhaC, it is located at the tip of L6 reaching the periplasm. Replacement by Ala of the invariant Arg dramatically affects the secretion efficiency, although the structure of FhaC and its channel properties remain unaffected. This substitution affects the secretion mechanism at a step beyond the initial TpsA-TpsB interaction. Replacement of the conserved Tyr affects the channel properties, but not the secretion activity, suggesting that this residue stabilizes the loop in the resting conformation of FhaC. Thus, the conserved motif at the tip of L6 represents an important piece of two-partner secretion machinery. This motif is conserved in a predicted loop between two β-barrel strands in more distant relatives of FhaC involved in protein transport across or assembly into the outer membranes of bacteria and organelles, suggesting a conserved function in the molecular mechanism of transport.
Two Faces of Hydrogen in Yttrium Hydroxyhydride: Y2H3O(OH) – a New Inorganic Chiral System with Hydridic and Protonic Hydrogens (2018)

Design of inorganic compounds containing different anions attracts a lot of attention because it affords a great opportunity to develop new functionality across the whole range of material properties. Based on the results of structure-modeling studies of a mixed-anion system, we predicted novel derivatives of oxyhydrides – chiral hydroxyhydrides M2H3O(OH) (M = Y, Sc, La, and Gd) that are characterized by the coexistence of three anionic species, H–, O2 –, and OH– inside the crystal lattice. The materials demonstrate a speciﬁc charge ordering, which is connected with the chiral organization of atoms where both the metal cations and the anions are standing in positions that form helical curves spreading along the tetragonal axis. Moreover, the twisting of the H– and H+ sites gives rise to their linking via strong dihydrogen bonds. Unusual structural, electron and optical features caused by the P41 crystal structure have been investigated in the Y2H3O(OH) comprehensive case study.
Probabilistic timing analysis on conventional cache designs (2013)

Probabilistic timing analysis (PTA), a promising alternative to traditional worst-case execution time (WCET) analyses, enables pairing time bounds (named probabilistic WCET or pWCET) with an exceedance probability (e.g., 10-16), resulting in far tighter bounds than conventional analyses. However, the applicability of PTA has been limited because of its dependence on relatively exotic hardware: fully-associative caches using random replacement. This paper extends the applicability of PTA to conventional cache designs via a software-only approach. We show that, by using a combination of compiler techniques and runtime system support to randomise the memory layout of both code and data, conventional caches behave as fully-associative ones with random replacement.
Fidelity of dna replication (1979)

To maintain species identity, DNA replication must be an exceptionally faithful process. The only inac-curacies tolerated would be those infrequent mutations that provide for species diversity. On the basis of spon-taneous mutation rates in prokaryotic and eukaryotic cells, it is usually estimated that stable misincorpora-tion of a base during DNA replication occurs with a frequency of 10-8-10-11/bp synthesized (Drake 1969). This accuracy appears to be achieved by a multistep process (Table 1). First, the difference in free energy (-AG) for correct over incorrect Watson-Crick base pairings results from little more than one hydrogen bond (2-3 kcal). This accounts for an error rate of approximately 10-2 (Mildvan 1974; Loeb et al. 1974; Hopfield 1974). Second, DNA
Thiol Depletion Induces Apoptosis in Cultured Lung Fibroblasts (1999)

Thiol antioxidants are implicated in the protection of cells from oxidative injury. We studied the role of thiols in the regulation of apoptosis in cultured lung fibroblasts. Thiol depletion by culturing fibroblasts in cystine-free medium or with thiol-depleting agents induced oxidant accumulation and cell death by apoptosis. The cell death was prevented by the antioxidants ascorbic acid (AA) and catalase. Thiol depletion also induced leukotriene (LT) C4, LTD4, and LTE4 production and selective phosphorylation of p38-mitogen-activated protein kinase (MAPK) and its nuclear substrate ATF2. LT production and p38-MAPK phosphorylation were required for induction of apoptosis because thiol depletion-induced apoptosis was completely blocked by the 5-lipoxygenase inhibitor AA861, the LT antagonists FPL55712 and ONO1078, and the p38-MAPK inhibitor SB203580. LT production was inhibited by AA and p38-MAPK phosphorylation was inhibited by AA, AA861, and FPL55712. In an in vitro scratch wound model, repopulating fibroblasts at the wound margin, but not quiescent cells at the intact site, selectively underwent thiol depletion- induced apoptosis that was completely blocked by AA861, FPL55712, and SB203580. Thus, thiol depletion induces apoptosis through an ordered pathway involving oxidant accumulation, LT production, and p38-MAPK activation. Apoptosis of wound fibroblasts may be responsible for impaired wound healing in various organs, including the lung.
Antibody-Based Therapies in Infectious Diseases (2000)

Before antibiotics, sera from immune animals and humans were used to treat a variety of infectious diseases, often with successful results. In the beginning of the 20th century, serum therapy had taken a place in standard treatment protocols for several infectious diseases, such as meningitis, diphtheria, tetanus, and lobar pneumonia. As early as 1906, antimeningococcal serum was intravenously used as a treatment for meningitis, since it was proved to cross the blood-brain barrier. However, treatment with meningococcal antiserum was shown to be ineffective, because available antiserum was only effective against type A meningococcus, whereas type C was a more common cause of meningococcal meningitis (1). Several trials demonstrated that application of type-specific antipneumococcal serum reduced mortality in patients with lobar pneumonia by about 50%, from 30-40% to 10-20% (2). Several successes with immune serum were observed in treatment and prevention of other infectious diseases, which include Haemophilus influenzae meningitis, measles, diphtheria, hepatitis A and B, poliovirus infection, and cytomegalovirus (CMV) infection (1). However, numerous problems have been observed with immune sera, including lot-to-lot variations characterized with variable amounts of specific antibodies, occurrence of serum sickness as a complication, and some hazards in transmission of some infectious diseases (3,4).
Cognitive Engine Design for Link Adaptation: An Application to Multi-Antenna Systems (2010)

In this paper, we present a Cognitive Engine (CE) design for link adaptation and apply it to a system which can adapt its use of multiple antennas in addition to modulation and coding. Our design moves forward the state of the art in several ways while having a simple structure. Specifically, the CE only needs to observe the number of successes and failures associated with each set of channel conditions and communication method. From these two numbers, the CE can derive all of its functionality. First, it can estimate confidence intervals of the packet success rate (PSR) using the Beta distribution. A low computational approximation to the CDF of the Beta distribution is also presented. Second, the designed CE balances the tradeoff between learning and short-term performance (exploration {vs.} exploitation) by applying the Gittins index. Third, the CE learns the radio abilities independently of the operation objectives. Thus, if an objective changes, information regarding the radio's abilities is not lost. Finally, prior knowledge such as capacity, BER curves, and basic communication principles are used to both initialize the CE's knowledge and maximize the learning rate across different channel conditions. The proposed CE is demonstrated to have the ability to learn in a dynamic scenario and quickly approach maximal performance.
Directed supramolecular assembly of Cu(ii)-based “paddlewheels” into infinite 1-D chains using structurally bifunctional ligands (2005)

The construction of Cu(II)-containing supramolecular chains is achieved by combining suitable anionic ligands (for controlling the coordination geometry and for creating a neutral building block) with four new bifunctional ligands containing a metal-coordinating pyridyl site and a self-complementary hydrogen-bonding moiety. Seven crystal structures are presented and in each case, the copper(II) complex displays a "paddlewheel" arrangement, with four carboxylate ligands occupying the equatorial sites, leaving room for the bifunctional ligand to coordinate in the axial positions. The supramolecular chemistry, which organizes the coordination-complexes into the desired infinite 1-D chains, is driven by a combination of N-H...N and N-H...O hydrogen-bonds in five of the seven structures.
Navigation in hybrid metric-topological maps (2011)

We present an approach for navigation in hybrid maps consisting of a topological graph overlaid with local occupancy grids. The topological graph is built on top of a graph SLAM system, which can be efficiently optimized even for very large environments. The novel feature of our system is that it navigates locally using local metric maps, while the overall plan is formed on the topological graph. Unlike many current SLAM methods, we never reconstruct a full occupancy grid of the environment for localization or path planning. We show that our method generates near-optimal plans, and deals gracefully with changes to the map.
Focusing with planar microlenses made of two-dimensionally varying high contrast gratings (2014)

We report on the focusing performance of reflective two-dimensionally varying high contrast grating lenses based on silicon. The combination of their subwavelength nature and their high refractive index contrast makes it possible to create highly tolerant and planar microlenses. We used a rigorous mathematical code to design the lenses and verified their performance with finite element simulations. We also investigated the effects of grating thickness, angle, and wavelength of incidence in these simulations. Experimentally, we show the evolution of the beam profile along the optical axis for a lens with a high (0.37) numerical aperture. We have explored a wide range of numerical apertures (0.1–0.93) and show that the lenses behave as expected across the full range. Our analyses demonstrate the large design flexibility with which these lenses can be made along with ease of fabrication and potential for a number of applications in micro-optics.
Sexual dimorphism in glioma glycolysis underlies sex differences in survival (2017)

The molecular bases for sex differences in cancer remain undefined and how to incorporate them into risk stratification remains undetermined. Given sex differences in metabolism and the inverse correlation between fluorodeoxyglucose (FDG) uptake and survival, we hypothesized that glycolytic phenotyping would improve glioma subtyping. Using retrospectively acquired lower-grade glioma (LGG) transcriptome data from The Cancer Genome Atlas (TCGA), we discovered male-specific decreased survival resulting from glycolytic gene overexpression. Patients within this high-glycolytic group showed significant differences in the presence of key genomic alterations (i.e., 1p/19q codeletion, CIC, EGFR, NF1, PTEN, FUBP1, and IDH mutations) compared with the low-glycolytic group. Although glycolytic stratification defined poor prognostic males independent of grade, histology, TP53, and ATRX mutation status, we unexpectedly found that females with high-glycolytic gene expression and wild-type IDH survived longer than all other wild-type patients. Validation with an independent metabolomics dataset from grade 2 gliomas determined that glycolytic metabolites selectively stratified males and also uncovered a potential sexual dimorphism in pyruvate metabolism. These findings identify a potential synergy between patient sex, tumor metabolism, and genomic alterations in determining outcome for glioma patients.
Clinical and genomic characterisation of mismatch repair deficient pancreatic adenocarcinoma (2020)

MMRD pancreatic cancers have distinct clinical, pathological and genomic profiles. Patients with MMRD pancreatic cancer should be considered for basket trials targeting enhanced immunogenicity or the unique genomic drivers in these malignancies.
Investigational treatment of rheumatoid arthritis with a vibrotactile device applied to the external ear (2019)

ClinicalTrials.gov Identifier: NCT01569789 and NCT00859859. The AMC trial conducted in The Netherlands does not have a ClinicalTrials.gov Identifier.
Ruthenium Nitrosyls Derived from Tetradentate Ligands Containing Carboxamido-N and Phenolato-O Donors: Syntheses, Structures, Photolability, and Time Dependent Density Functional Theory Studies (2010)

In order to examine the role(s) of designed ligands on the NO photolability of {Ru-NO}(6) nitrosyls, a set of three nitrosyls with ligands containing two carboxamide groups along with a varying number of phenolates have been synthesized. The nitrosyls namely, (NEt(4))(2)[(hybeb)Ru(NO)(OEt)] (1), (PPh(4))[(hypyb)Ru(NO)(OEt)] (2), and [(bpb)Ru(NO)(OEt)] (3) have been characterized by X-ray crystallography. Complexes 1-3 are diamagnetic, exhibit nu(NO) in the range 1780-1840 cm(-1) and rapidly release NO in solution upon exposure to low power UV light (7 mW/cm(2)). Density Functional Theory (DFT) and Time Dependent DFT (TDDFT) calculations on 1-3 indicate considerable contribution of ligand orbitals in the MOs involved in transitions leading to NO photolability. The results of the theoretical studies match well with the experimental absorption spectra as well as the parameters for NO photorelease and provide insight into the transition(s) associated with loss of NO.
53.2: Alkali & Alkaline‐Earth Metal Sources for OLED Devices (2006)

Abstract Electron injection in OLED organic layers is improved by using alkaline‐earth or alkali metals as cathode layers or as dopants inside organic layers. An innovative metal dispensing technology has been developed to overcome handling problems and to ensure controlled and reliable metal layers deposition for OLEDs.
Clay Stabilization in Low-Permeability Formations (1989)

ABSTRACT Clay stabilizers have been used in various forms in oil well treating solutions for over 30 years. Cationic organic polymers have been the most popular type stabilizer in use recently because of their resistance to wash-off and chemical attack, ease of application, and effectiveness in moderate to high permeability formations. Recent studies investigating the effectiveness of such stabilizers in very low to low permeability sandstones have shown them to be less than 100% effective in stabilizing clays to prevent swelling and migration. Results indicate that higher molecular weight polymers can create permeability impairment when injected into these formations. These findings indicated the need for further research into clay stabilizers. This research led to the development of a novel clay stabilizing chemical for low, as well as high, permeability formations. This low permeability clay stabilizer also offers additional benefits in treating low permeability formations by enhancing fluid recovery after fracturing, and preventing the detrimental effects of fracturing fluid gel adsorption onto formation surfaces.
Enantioselective Synthesis of 1-Ferrocenylalkylamines via 1,2-Addition of Organolithium Compounds to Ferrocenecarboxaldehyde-SAMP-Hydrazone (1996)

Nucleophilic 1,2-addition of organolithium compounds to ferrocenecarboxaldehyde-SAMP-hydrazone 2 leads to hydrazines 3 in almost quantitative yields and with virtually complete asymmetric induction (de ≥ 98%). Subsequent N-N bond cleavage via Raney-nickel promoted hydrogenolysis gives 1-ferrocenylalkylamines 4 in good overall yields (30-54%, 4 steps) and with high enantiomeric excesses (ee = 85-94%). The absolute configuration was determined by X-ray structure analysis of hydrazine (S,R)-3d.
Equivalence of ML decoding to a continuous optimization problem (2020)

Maximum likelihood (ML) and symbolwise maximum aposteriori (MAP) estimation for discrete input sequences play a central role in a number of applications that arise in communications, information and coding theory. Many instances of these problems are proven to be intractable, for example through reduction to NP-complete integer optimization problems. In this work, we prove that the ML estimation of a discrete input sequence (with no assumptions on the encoder/channel used) is equivalent to the solution of a continuous non-convex optimization problem, and that this formulation is closely related to the computation of symbolwise MAP estimates. This equivalence is particularly useful in situations where a function we term the expected likelihood is efficiently computable. In such situations, we give a ML heuristic and show numerics for sequence estimation over the deletion channel.
Meta‐analysis of digital dermoscopy follow‐up of melanocytic skin lesions: a study on behalf of the International Dermoscopy Society (2012)

It has been demonstrated that dermoscopic monitoring of melanocytic lesions allows for the recognition of melanoma in early stages while minimizing the excision of benign lesions. However, it is still pending to determine the real impact of digital follow-up in the clinical management of pigmented lesions. To assess the evidence of follow-up of melanocytic skin lesions with digital dermoscopy in the management of individuals at risk for melanoma by performing a meta-analysis. Medline database was screened, no limits in terms of date or language were applied. Original studies were selected when the following criteria were met: performed in clinical setting with clinical and dermoscopic evaluation made by physicians, data regarding population characteristics included, follow-up strategy used described. Fourteen of 145 retrieved references were retained. Included studies account for a total of 5787 patients (mean 445 per study) and 52,739 lesions monitored (mean per study 4057; range 272-11,396) with a mean of 12 lesions monitored per patient; a total of 4388 lesions (8.3%) were excised. The mean length of follow-up was 30 months. A mean of <1 lesion was excised per patient along the surveillance period. The number needed to monitor (NNM) ranged from 31 to 1008 (mean: 348) among eligible studies. For every additional month of monitoring, 1additional melanoma was detected. Using digital dermoscopy follow-up, the proportion of in situ melanoma and thin melanomas are higher than expected in general population. Chances to detect a melanoma during surveillance increase as the length of follow-up extends.
RESEARCH ARTICLE Evaluation of ( 111 In)-Labeled Zinc-Dipicolylamine Tracers for SPECT Imaging of Bacterial Infection (2015)

Purpose: This study prepared three structurally related zinc–dipicolylamine (ZnDPA) tracers with [ 111 In] labels and conducted biodistribution and single-photon emission computed tomography/ computed tomography (SPECT/CT) imaging studies of a mouse leg infection model. Procedures: Two monovalent tracers, ZnDPA-[ 111 In]DTPA and ZnDPA-[ 111 In]DOTA, each with a single zinc–dipicolylamine targeting unit, and a divalent tracer, Bis(ZnDPA)-[ 111 In]DTPA, with two zinc–dipicolylamine units were prepared. Organ biodistribution and SPECT and CT imaging studies were performed on living mice with a leg infection created by injection of clinically relevant Gram positive Streptococcus pyogenes. Fluorescent and luminescent Eu 3+ -labeled versions of these tracers were also prepared and used to measure relative affinity for the exterior membrane surface of bacterial cells and mimics of healthy mammalian cells. Results: All three 111 In-labeled radiotracers were prepared with a radiopurity of 990 %. The biodistribution studies showed that the two monovalent tracers were cleared from the body through the liver and kidney, with retained percentage injected dose for all organs of G 8%a t 20 h and infected leg target to non-target ratio (T/NT) ratio of ≤3.0. Clearance of the divalent tracer from the bloodstream was slower and primarily through the liver, with a retained percentage injected dose for all organs G37 % at 20 h and T/NT ratio rising to 6.2 after 20 h. The SPECT/CT imaging indicated the same large difference in tracer pharmacokinetics and higher accumulation of the divalent tracer at the site of infection. Conclusions: All three [ 111 In]-ZnDPA tracers selectively targeted the site of a clinically relevant mouse infection model that could not be discerned by visual external inspection of the living animal. The highest target selectivity, observed with a divalent tracer equipped with two zinc–dipicolylamine targeting units, compares quite favorably with the imaging selectivities previously reported for other nuclear tracers that target bacterial cell surfaces. The tracer pharmacokinetics depended heavily on tracer molecular structure suggesting that it may be possible to rapidly fine tune the structural properties for optimized in vivo imaging performance and clinical translation.
Genetic algorithm synthesis of impedance-matched infrared ZIMs with wide FOV using a generalized inversion algorithm (2010)

In this paper, the authors present an impedance-matched low loss infrared zero index metamaterials (ZIM) with a wide field-of-view. The ZIM structure is optimized by a genetic algorithm combined with a generalized inversion method capable of retrieving the effective anisotropic constitutive parameters of the metamaterial with its angular response considered.
MRI-Compatible Robotics (2008)

The eight articles in this special issue focus on MRI-compatible robotics. The articles are summarized here.