gebhart/patrepeval huggingface dataset:
Unified crowd segmentation (2008)

Abstract. This paper presents a unified approach to crowd segmenta-tion. A global solution is generated using an Expectation Maximization framework. Initially, a head and shoulder detector is used to nominate an exhaustive set of person locations and these form the person hypothe-ses. The image is then partitioned into a grid of small patches which are each assigned to one of the person hypotheses. A key idea of this paper is that while whole body monolithic person detectors can fail due to oc-clusion, a partial response to such a detector can be used to evaluate the likelihood of a single patch being assigned to a hypothesis. This captures local appearance information without having to learn specific appearance models. The likelihood of a pair of patches being assigned to a person hypothesis is evaluated based on low level image features such as uni-form motion fields and color constancy. During the E-step, the single and pairwise likelihoods are used to compute a globally optimal set of assign-ments of patches to hypotheses. In the M-step, parameters which enforce global consistency of assignments are estimated. This can be viewed as a form of occlusion reasoning. The final assignment of patches to hy-potheses constitutes a segmentation of the crowd. The resulting system provides a global solution that does not require background modeling and is robust with respect to clutter and partial occlusion. 1
Post-transcriptional regulation of microRNA expression (2006)

microRNAs (miRNAs) are endogenous, noncoding approximately 22-nucleotide RNA molecules that have recently emerged as fundamental, post-transcriptional regulators of cognate target gene expression. Many mammalian miRNAs are expressed in a tissue-specific manner, a phenomenon that has so far been attributed to transcriptional regulation. We here show by Northern blots and in situ hybridization experiments that the expression of mammalian miRNAs can be regulated at the post-transcriptional level. In particular, miR-138 is spatially restricted to distinct cell types, while its precursor, pre-miR-138-2, is ubiquitously expressed throughout all tissues analyzed. Furthermore, pre-miR-138-2 is exported from the nucleus to the cytoplasm, suggesting that cleavage of this pre-miRNA by Dicer is restricted to certain tissues and cell types. Thus, differential processing of pre-miRNAs might be an alternative mechanism to control miRNA function.
Simple and quick chemical aminoacylation of tRNA in cationic micellar solution under ultrasonic agitation (2005)

A simple and quick method for direct aminoacylation of a tRNA with a non-natural amino acid was developed by using an N-protected amino acid cyanomethyl ester as a substrate solubilized in CTACl micelle under ultrasonic agitation.
Diffraction effects in the parametric interaction of acoustic waves: application to measurements of the nonlinearity parameter B/A in liquids (2001)

This paper deals with diffraction effects related to the determination of nonlinearity parameters B/A in liquids using the parametric interaction. A diffraction model, based on plane wave expansions, is applied to weak nonlinear interactions between two ultrasonic waves propagating in an absorbing medium. A validation of the model has been carried out with an experiment performed using an optical interferometer. A method is proposed to measure nonlinearity parameters with the parametric interaction of two waves with a high frequency ratio. With respect to diffraction effects, the parametric interaction can then be identified with a phase modulation of the high frequency wave. A prototype, using the interaction of a 30-MHz frequency continuous wave with an acoustic pulse of central frequency 2.5 MHz, has been designed. The proposed method is validated by nonlinearity parameters measurements in well-known liquids (water and ethanol). The uncertainty on absolute measurements is discussed, and a relative method is proposed to increase the accuracy. This method enables measurements without any transducer calibration.
Safety of Withholding Heparin in Pregnant Women with a History of Venous Thromboembolism (2000)

The risk of recurrent antepartum venous thromboembolism in women with a history of venous thromboembolism is low, and therefore routine antepartum prophylaxis with heparin is not warranted.
Ancient conserved domains shared by animal soluble guanylyl cyclases and bacterial signaling proteins (2003)

The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals. The HNOBA domain functionally interacts with the HNOB domain, and possibly binds a ligand, either in cooperation, or independently of the latter domain. Phyletic profiles and phylogenetic analysis suggest that the HNOB and HNOBA domains were acquired by the animal lineage via lateral transfer from a bacterial source.
von Willebrand factor biosynthesis, secretion, and clearance: connecting the far ends (2015)

To understand the placement of a certain protein in a physiological system and the pathogenesis of related disorders, it is not only of interest to determine its function but also important to describe the sequential steps in its life cycle, from synthesis to secretion and ultimately its clearance. von Willebrand factor (VWF) is a particularly intriguing case in this regard because of its important auxiliary roles (both intra- and extracellular) that implicate a wide range of other proteins: its presence is required for the formation and regulated release of endothelial storage organelles, the Weibel-Palade bodies (WPBs), whereas VWF is also a key determinant in the clearance of coagulation factor VIII. Thus, understanding the molecular and cellular basis of the VWF life cycle will help us gain insight into the pathogenesis of von Willebrand disease, design alternative treatment options to prolong the factor VIII half-life, and delineate the role of VWF and coresidents of the WPBs in the prothrombotic and proinflammatory response of endothelial cells. In this review, an update on our current knowledge on VWF biosynthesis, secretion, and clearance is provided and we will discuss how they can be affected by the presence of protein defects.
Optimal Design of an “Energy Tower” Power Plant (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> The Energy Tower (ET) is a power plant that uses seawater and solar energy accumulated in hot dry desert air to produce electricity. An optimization algorithm was designed and programmed for the design of an ET that also includes water reservoirs, pipes, and pumps. The algorithm is a variant of the block coordinate descent method, where one subproblem is formulated as a linear programming problem, and a second subproblem usually has an analytic solution. If the analytic solution is nonfeasible, a variant of the quasi-Newton algorithm is used instead. The algorithm was tested with input information from the arid area near Eilat, the Red Sea, Israel. </para>
Production of a Recombinant Major Inner Capsid Protein for Serological Detection of Epizootic Hemorrhagic Disease Virus (2005)

Constructs of the major core protein, designated VP7, from epizootic hemorrhagic disease virus (EHDV) type 1 were made by amino- or carboxyl-terminal fusion of a six-histidine residue tag to the VP7-1 gene. The resulting fusion proteins were produced in a baculovirus expression system and purified by a rapid, one-step procedure using nickel-nitrilotriacetic acid technology. A high level of VP7-1 protein expression was detected with the N-terminal six-histidine tag fusion construct and was comparable to the level of expression observed with an untagged VP7-1 Bam construct. In contrast, the inclusion of a six-histidine tag at the C terminus adversely affected protein expression. The antigenicity of the N-terminal six-histidine tag EHDV VP7-1 product was identical to that observed with the native virus antigen and untagged EHDV VP7-1 recombinant protein, as determined by reactivity with EHDV specific antibodies in an enzyme-linked immunosorbent assay (ELISA) and Western blot. The high production and purity levels that can be attained for the N-terminal six-histidine tag VP7-1 protein and its reactivity with EHDV-specific sera in a competitive ELISA make it a suitable assay reagent.
Multi-wavelength fiber networks (2003)

This paper describes the main trends and design issues in the design of current generation of WDM optical networks, and the enabling factors and motivations that will push to build the next generation transport networks. The latter will benefit from new optical technologies (ultra-long haul, switching,…) to reduce the network cost, and from new control technologies (Generalised Multi-Protocol Label Switching) that will make them dynamically flexible to better serve the changing traffic demands of emerging services. The paper covers all aspects of the network: network design and planning, system and architecture design, technologies, control and management. It also includes an overview of current state of the art and observations/statistics learnt from network studies.
Media Modulation based Molecular Communication (2022)

In conventional molecular communication (MC) systems, the signaling molecules used for information transmission are stored, released, and then replenished by a transmitter (TX). However, the replenishment of signaling molecules at the TX is challenging in practice. Furthermore, in most envisioned MC applications, e.g., in the medical field, it is not desirable to insert the TX into the MC system, as this might impair natural biological processes. In this paper, we propose the concept of media modulation based MC where the TX is placed outside the channel and utilizes signaling molecules already present inside the system. The signaling molecules can assume different states which can be switched by external stimuli. Hence, in media modulation based MC, the TX modulates information into the state of the signaling molecules. In particular, we exploit the group of photochromic molecules, which undergo light-induced reversible state transitions, for media modulation. We study the usage of these molecules for information transmission in a three-dimensional duct system, which contains an eraser, a TX, and a receiver for erasing, writing, and reading of information via external light, respectively. We develop a statistical model for the received signal which accounts for the distribution of the signaling molecules in the system, the initial states of the signaling molecules, the reliability of the state control mechanism, the randomness of irrepressible, spontaneous state switching, and the randomness of molecule propagation. We adopt a maximum likelihood detector and a threshold based detector. Furthermore, we derive analytical expressions for the optimal threshold value and the resulting bit error rate (BER), respectively. Our results reveal that media modulation enables reliable information transmission, validating it as a promising alternative to MC based on molecule emitting TXs.
Electronic Structure of Pyrochlore Iridates: From Topological Dirac Metal to Mott Insulator (2010)

In 5d transition metal oxides such as the iridates, novel properties arise from the interplay of electron correlations and spin-orbit interactions. We investigate the electronic structure of the pyrochlore iridates, (such as Y$_{2}$Ir$_{2}$O$_{7}$) using density functional theory, LDA+U method, and effective low energy models. A remarkably rich phase diagram emerges on tuning the correlation strength U. The Ir magnetic moment are always found to be non-collinearly ordered. However, the ground state changes from a magnetic metal at weak U, to a Mott insulator at large U. Most interestingly, the intermediate U regime is found to be a Dirac semi-metal, with vanishing density of states at the Fermi energy. It also exhibits topological properties - manifested by special surface states in the form of Fermi arcs, that connect the bulk Dirac points. This Dirac phase, a three dimensional analog of graphene, is proposed as the ground state of Y$_{2}$Ir$_{2}$O$_{7}$ and related compounds. A narrow window of magnetic `axion' insulator, with axion parameter $θ=π$, may also be present at intermediate U. An applied magnetic field induces ferromagnetic order and a metallic ground state.
First-Order Magnetic Phase Transitions in Fe (1981)

The first observation of a first-order phase transition in the magnetization of Fe in an applied field is reported. The samples were epitaxially grown (110) Fe films on GaAs. Mean-field theory, with the inclusion of uniaxial anisotropy and the constraint that $\stackrel{\ensuremath{\rightarrow}}{\mathrm{M}}$ lie in the plane of the film, gives excellent agreement with the observed transition. The relationship of this transition to the predictions of the three-state Potts model for cubic ferromagnets is discussed.
Transient Ordered Phases in a Two-Dimensional Ternary System (1999)

The kinetics of a ternary system for the square lattice are investigated using the cluster variation method and the path probability method in the pair approximation. It is shown that the differences in the diffusive jump rates for the three atomic species of a ternary system has a strong effect on the kinetics of the system. The kinetic paths of ordering and disordering classified according to the phase diagram are calculated. From the study of the kinetics of ordering and disordering, it is shown that there are two types of transient ordered phases during the relaxation from the disordered state to the equilibrium disordered state. It is also shown that there are overshooting effects in the evolution of long range ordering parameters in the kinetics of ordering for a ternary system on the square lattice.
Combination therapy with subcutaneous interleukin-2 and interferon-alpha in advanced renal cancer patients with poor prognostic factors. (1996)

Sixteen patients with metastatic renal cell carcinoma were treated with a combination of low-dose subcutaneous interleukin-2 (IL-2) and recombinant interferon (IFN)-alpha. One treatment course included 6 weeks of treatment followed by a 2-week rest. Patients received therapy as outpatients. All patients were assessable for toxicity and response assessment. Nine patients experienced severe toxicities resulting in dosage modification. The major treatment-limiting side effects were gastrointestinal, cutaneous, fever and flu-like symptoms. One patient (6%) had partial remission and six patients (37.5%) had disease stabilization. Overall median survival was 8 months. In our study IL-2 and IFN-alpha showed a low activity and a quite high toxicity. It seems that the prognostic factors per se rather than treatment options might impact the treatment results in advanced renal cancer patients.
Global patterns of genomic and phenotypic variation in the invasive harlequin ladybird (2023)

Our study on H. axyridis provides new insights into its invasion processes into other major continents from its native Asian range, reconstructs a geographic range evolution across its native region China, and tentatively suggests that its invasiveness may differ between mitochondrial haplotypes.
Large-Area 2D Covalent Organic Framework Membranes with Tunable Single-Digit Nanopores for Predictable Mass Transport (2022)

The potential of covalent organic frameworks (COFs) for molecular separations remains unrealized because of challenges transforming nanoscale COF materials into large-area functional COF membranes. Herein, we report the synthesis of large-area (64 cm<sup>2</sup>), ultrathin (24 nm), β-ketoenamine-linked 2D COFs using a facile interfacial polymerization technique. Angstrom-level control over single-digit nanopore size (1.4-2.0 nm) is achieved by direct integration of variable-length monomers. We apply these techniques to fabricate a series of large-area 2D COF membranes with variable thicknesses, pore sizes, and supporting materials. Tunable 2D COF properties enable control over COF membrane mass transport, resulting in high solvent fluxes and sharp molecular weight cutoffs. For organic solvent nanofiltration, the 2D COF membranes demonstrate an order-of-magnitude greater permeance than the state-of-the-art commercial polymeric membrane. We apply continuum models to quantify the dominance of pore passage resistance to mass transport over pore entrance resistance. A strong linear correlation between single-digit nanopore tortuosity and 2D COF thickness enables solvent fluxes to be predicted directly from solvent viscosity and COF membrane properties. Solvent-nanopore interactions characterized by the membrane critical interfacial tension also appear to influence mass transport. The pore flow transport model is validated by predicting the flux of a 52 nm thick COF membrane.
Visualizing Vpr-Induced G2 Arrest and Apoptosis (2014)

Vpr is an accessory protein of human immunodeficiency virus type 1 (HIV-1) with multiple functions. The induction of G2 arrest by Vpr plays a particularly important role in efficient viral replication because the transcriptional activity of the HIV-1 long terminal repeat is most active in G2 phase. The regulation of apoptosis by Vpr is also important for immune suppression and pathogenesis during HIV infection. However, it is not known whether Vpr-induced apoptosis depends on the ability of Vpr to induce G2 arrest, and the dynamics of Vpr-induced G2 arrest and apoptosis have not been visualized. We performed time-lapse imaging to examine the temporal relationship between Vpr-induced G2 arrest and apoptosis using HeLa cells containing the fluorescent ubiquitination-based cell cycle indicator2 (Fucci2). The dynamics of G2 arrest and subsequent long-term mitotic cell rounding in cells transfected with the Vpr-expression vector were visualized. These cells underwent nuclear mis-segregation after prolonged mitotic processes and then entered G1 phase. Some cells subsequently displayed evidence of apoptosis after prolonged mitotic processes and nuclear mis-segregation. Interestingly, Vpr-induced apoptosis was seldom observed in S or G2 phase. Likewise, visualization of synchronized HeLa/Fucci2 cells infected with an adenoviral vector expressing Vpr clearly showed that Vpr arrests the cell cycle at G2 phase, but does not induce apoptosis at S or G2 phase. Furthermore, time-lapse imaging of HeLa/Fucci2 cells expressing SCAT3.1, a caspase-3-sensitive fusion protein, clearly demonstrated that Vpr induces caspase-3-dependent apoptosis. Finally, to examine whether the effects of Vpr on G2 arrest and apoptosis were reversible, we performed live-cell imaging of a destabilizing domain fusion Vpr, which enabled rapid stabilization and destabilization by Shield1. The effects of Vpr on G2 arrest and subsequent apoptosis were reversible. This study is the first to characterize the dynamics of the morphological changes that occur during Vpr-induced G2 arrest and apoptosis.
Optimization of interferometric photonic cells for biochemical sensing based on advanced high sensitivity optical techniques (2008)

The integration between micro-nano fluidics and optics is a new emerging research field, with promising high impact applications in the area of optical biosensing devices. This is the case of tunable Mach-Zehnder interferometers, photonic crystals and ring resonators, which have been demonstrated recently. Recent investigations1 have demonstrated that by combination of the simultaneous used of Ellipsometry, Reflectometry and Spectrometry based technologies broadly used in semiconductor industry at sub-micron spot-size level and advanced photonic structures, a relevant improvement can be achieved at the level of performance of the current state of the art for label-free biosensing and nano-fluidics metrology. The variation in the effective index of refraction can be easily detected in micron/sub-micron domains due to the fact of using several reflectivity profiles and optical responses simultaneously, making possible to remove ambiguities in the sensing interrogation process. To achieve this novel bio-chemical sensing system, it is proposed to combine the miniaturization of sub-micro-holes based Interferometric photonic structures in combination with sub-micron spot size advance optical techniques holistically. Thus, optical sensing system is based on the observation of external reflectivity profile of the high sensitive photonic structures. The reflectivity profile provides four magnitudes which can be used to assess the photonic structures response. These are the reflected amplitude and phase of the electric field components polarized parallel (p) and perpendicular (s) to the plane incidence. The reflected light of the photonic structures produce spectra interference patterns as a function of the angle of incidence for p and s polarization directions and as a function of the spectral range. These patterns are the fundamental source of information to detect the biomolecules binding in the sensing surfaces, ultra small fraction of volumes and flow control in sub-micron domains. Theoretical calculations at CLUPM demonstrate that a detection limit of 10-7 R.I.U. and surface concentration detection limit of 0.1 pg/mm2 are feasible.
An open chat with…Alexander Wlodawer (2022)

Alexander Wlodawer has been a member of the FEBS Open Bio Editorial Board since the journal's launch in 2011. Currently, he is Senior Investigator at the Center for Structural Biology, National Cancer Institute in Frederick, Maryland, USA. He received his Ph.D. from the University of California, Los Angeles in 1974, completed postdoctoral training at Stanford University and has also worked at the National Bureau of Standards, the ABL-Basic Research Program at the NCI-FCRDC and the University of Cambridge, UK. He is Doctor Honoris Causa of the Technical University of Lodz, Poland. Alexander Wlodawer is also a recipient of the 2006 NCI Mentor of Merit Award, was awarded the Heyrovsky Honorary Medal by the Czech Academy of Sciences in 2008, was elected Foreign Member of the Polish Academy of Sciences in 2005, and has been member of the Editorial Board of The FEBS Journal since 2007. He is currently Editor-in-Chief of the journal Current Research in Structural Biology. In this compelling interview, he shares with us his experiences on solving the structures of IL-4 and retroviral proteases, advice on how to deal with being scooped, and his thoughts on open data sharing and AlphaFold.
Endocrine Factors in Depression (1994)

After a thorough diagnostic evaluation, patients initially presenting with depression are often found to have an endocrine disorder.
Compressed sensing technique for high-resolution radar imaging (2008)

Compressed sensing (CS) has recently attracted much interest because of its important offerings and versatility. High-resolution radar imaging applications such as through-the-wall radar (TWR) imaging or inverse synthetic aperture radar (ISAR) are two key application areas that can greatly benefit from CS. Both applications require probing targets using radar signals with large bandwidth for collecting, and then processing, a large number of data samples for achieving high resolution imaging. These applications are also characterized by sparse imaging where targets of interest are few and have larger cross-section than clutter objects. Reducing the number of samples without compromising the imaging quality reduces the acquisition time and saves signal bandwidth. This reduction is important when surveillance is performed within small time window and when targets are required to remain stationary without translation or rotation motions, to avoid blurring and smearing of images. In this paper, we discuss applicability of compressed sensing to indoor radar imaging, using synthesized TWR data.