gebhart/patrepeval huggingface dataset:
Survival mechanisms for Streptomyces linear replicons after telomere damage (2002)

The ability of linear replicons to propagate their DNA after telomere damage is essential for perpetuation of the genetic information they carry. We introduced deletions at specific locations within telomeres of streptomycete linear plasmids and investigated mechanisms that enable survival. Here, we report that rescue of such plasmids in Streptomyces lividans occurs by three distinct types of events: (i) repair of the damaged telomere by homologous recombination; (ii) circularization of the plasmid by non-homologous end-to-end joining; and (iii) formation of long palindromic linear plasmids that duplicate the intact telomere by a non-recombinational process. The relative frequency of use of these survival mechanisms depended on the location and length of the telomeric DNA deletion. Repair by intermolecular recombination between the telomeres of chromosomes and plasmids, deletion of additional DNA during plasmid circularization, and insertion of chromosomal DNA fragments into plasmids during end-to-end joining were observed. Our results show that damage to telomeres of Streptomyces linear replicons can promote major structural transformations in these replicons as well as genetic exchange between chromosomes and extrachromosomal DNA. Our findings also suggest that spontaneous circularization of linear Streptomyces chromosomes may be a biological response to instances of telomere damage that cannot be repaired by homologous recombination.
Toward Explainable Deep Anomaly Detection (2021)

Anomaly explanation, also known as anomaly localization, is as important as, if not more than, anomaly detection in many real-world applications. However, it is challenging to build explainable detection models due to the lack of anomaly-supervisory information and the unbounded nature of anomaly; most existing studies exclusively focus on the detection task only, including the recently emerging deep learning-based anomaly detection that leverages neural networks to learn expressive low-dimensional representations or anomaly scores for the detection task. Deep learning models, including deep anomaly detection models, are often constructed as black boxes, which have been criticized for the lack of explainability of their prediction results. To tackle this explainability issue, there have been numerous techniques introduced over the years, many of which can be utilized or adapted to offer highly explainable detection results.
Rescue of noncultivatable human r( during mixed infection with ts muta (2016)

Fastidious human rotaviruses that did not undergo productive infection in tissue culture were rescued by genetic reas- sortment during mixed infection with a temperature-sensitive (ts) mutant of a cultivatable bovine rotavirus. In this manner, the genes of the fastidious rotavirus that restricted growth in vitro were replaced by the corresponding genes from a tissue culture- adapted rotavirus. We recovered genetically reassorted viruses that grew to high titer and were neutralized specifically by hyper- immune guinea pig type 1 or type 2 human rotavirus antiserum. Preliminary RNA analysis of these clones disclosed that they were indeed viruses with reassorted genes.
Detailed, accurate, human shape estimation from clothed 3D scan sequences (2017)

We address the problem of estimating human pose and body shape from 3D scans over time. Reliable estimation of 3D body shape is necessary for many applications including virtual try-on, health monitoring, and avatar creation for virtual reality. Scanning bodies in minimal clothing, however, presents a practical barrier to these applications. We address this problem by estimating body shape under clothing from a sequence of 3D scans. Previous methods that have exploited body models produce smooth shapes lacking personalized details. We contribute a new approach to recover a personalized shape of the person. The estimated shape deviates from a parametric model to fit the 3D scans. We demonstrate the method using high quality 4D data as well as sequences of visual hulls extracted from multi-view images. We also make available BUFF, a new 4D dataset that enables quantitative evaluation (http://buff.is.tue.mpg.de). Our method outperforms the state of the art in both pose estimation and shape estimation, qualitatively and quantitatively.
Clonal Priming of Human Lymphocytes with Soluble Microbial Antigens: High‐Dose Paralysis, Restoration, and Autologous Leukocyte Preference (1978)

Lymphocytes stimulated in appropriate leukocyte cultures undergo blastogenesis and proliferation for a finite period of time. With specific antigens the proliferative response peaks usually between 4 and 8 days, after which the blastoid cells revert to small lymphocytes. Lymphocytes "primed" in this manner can be restimulated to proliferate only by the same antigen with which they were incubated and only with an adequate amount of a self-specific, autologous, somatic product(s). First or "primary" leukocyte cultures stimulated by optimal or supraoptimal concentrations of soluble protein antigens (purified protein derivative (PPD), tetanus toxoid, Candida albicans) will undergo proliferation in the first culture, but the increased number of small lymphocytes that can be visualized after 10--14 days often fail to respond to any stimulus in second (secondary) or "primed" cultures. However, when fresh X-irradiated autologous cells are re-added in appropriate amounts, vigorous accelerated proliferation takes place. Addition of allogeneic cells to antigen-primed populations has one of three effects: (1) no effect (complete restriction); (2) in some instances allogeneic cells restore a significant response to the specific antigen but almost never to the same degree as autologous cells; and (3) allogeneic cells can also induce high levels of accelerated responsiveness without added antigen. These findings are discussed in the context of a working hypothesis that self-specific factors are involved in all specific immune responses. The combination of antigen and self-specific factors may lead to a quantitatively unique immune response to all antigens in each individual. The preferential response to antigen in conjunction with autologous rather than allogeneic leukocytes suggests that self-specific products are required for recognition of soluble microbial antigens.
Constrained nonlinear minimum mse estimation (2008)

We address the problem of minimum mean-squared error (MMSE) estimation where the estimator is constrained to belong to a pre-defined set of functions. We derive a simple closed form formula that reveals the structure of the restricted estimator for a wide class of constraints. Using this formula we study various types of constrained estimation problems that arise commonly in the fields of signal processing and communication.
Data for comparative proteomics of ovaries from five non-model, crustacean amphipods (2015)

Ovaries were taken from five sexually mature amphipods: Gammarus fossarum, Gammarus pulex, Gammarus roeseli, Hyallela azteca and Parhyale hawaiensis. The soluble proteome extracted from individual pair of ovaries from five biological replicates was trypsin digested and the resulting peptides were analyzed by high resolution tandem mass spectrometry. The spectra were assigned with four protein sequence databases with different specificities: a RNAseq-derived G. fossarum database; a RNAseq-derived P. hawaiensis database; both originating from ovaries transcriptome; the Daphnia pulex database derived from whole-genome sequencing and the NCBInr database. The best interpretation was obtained for most animals with the specific RNA-seq protein database previously established by means of RNAseq carried out on G. fossarum. Proteins identified in the five amphipod species allow defining the core-proteome of female reproductive tissues of the Senticaudata suborder. The data accompanying the manuscript describing the database searches and comparative analysis Trapp et al., 2015 [1] have been deposited to the ProteomeXchange with identifiers PXD002253 (G. fossarum), PXD002254 (G. pulex), PXD002255 (G. roeseli), PXD002256 (H. Azteca), and PXD002257 (P. hawaiensis).
Mutations in RNU7-1 Weaken Secondary RNA Structure, Induce MCP-1 and CXCL10 in CSF, and Result in Aicardi-Goutières Syndrome with Severe End-Organ Involvement (2022)

Targeted RNU7-1 sequencing is recommended in genetically unexplained AGS cases. CSF cytokine profiling represents an additional diagnostic tool to identify aberrant IFN-I signaling. Clinical follow-up of RNU7-1-mutated patients should include screening for severe end-organ involvement including liver disease and nephropathy.
Design of a Gimbaled Compliant Mechanism Stage for Precision Motion and Dynamic Control in Z, ΘX and ΘY Directions (2004)

Obtaining precise motion control of a compliant mechanism is often hindered by competing kinematic, mechanic and dynamic requirements. Resonances limit the control bandwidth while compliance requirements limit the mechanism’s directional stiffness. This paper investigates the improvements possible for three-axis Z, θX and θY diaphragm flexure stages through the use of a design (T-Flex) with members complaint in bending and torsion. According to analytical modeling and FEA, the T-Flex is capable of removing problematic resonant modes of vibration without significantly increasing the axial or tilt stiffness. Bench-level experimentation was conducted on various configurations of compliant mechanisms to determine their effects on the motion characteristics for precision engineering applications. The results indicate that by pairing the T-Flex with a radially stiff compliant mechanism, gimbaled motion can be achieved, providing 7.0 nm/μm lateral cross-axis (parasitic) motions. The mechanism exhibits linear axial and tilt stiffness of 0.195 N/μm and 5.37×10−6 N-m/μrad, respectively. Dynamic testing agreed with the FEA prediction of the first natural frequency to within 10%. The T-Flex coupled with the stiff radial flexure has the potential to provide a precise three-axis configuration with a fundamental resonant frequency of 600 Hz.
Carlos Drummond de Andrade popularizante (2011)

A poética oral e popular atravessa toda a poesia de Carlos Drummond de Andrade, mas tem sido pouco notada e ainda menos estudada pela crítica do autor de Rosa do Povo (1945). Neste artigo procuramos mostrar de que modo este poeta, empenhado nas grandes questões históricas e sociais do seu tempo, constrói uma poesia que conjuga temas e formas populares com as tendências da arte moderna. Veremos alguns poemas em que é particularmente significativa a relação entre o quotidiano brasileiro, a visão do mundo e a expressão das classes ditas marginalizadas, e a ideologia e a linguagem do poeta.
Characterization of black carbon‐containing particles from soot particle aerosol mass spectrometer measurements on the R/V Atlantis during CalNex 2010 (2015)

Abstract We present mass spectrometry measurements of black carbon‐containing particles made on board the R/V Atlantis during the CalNex (California Research at the Nexus of Air Quality and Climate Change) 2010 study using an Aerodyne Research Inc. soot particle aerosol mass spectrometer (SP‐AMS). The R/V Atlantis was deployed to characterize air masses moving offshore the California coast and to assess emissions from sources in urban ports. This work presents a first detailed analysis of the size‐resolved chemical composition of refractory black carbon (rBC) and of the associated coating species (NR‐PM BC ). A colocated standard high‐resolution aerosol mass spectrometer (HR‐AMS) measured the total nonrefractory submicron aerosol (NR‐PM 1 ). Our results indicate that, on average, 35% of the measured NR‐PM 1 mass (87% of the primary and 28% of the secondary NR‐PM 1 , as obtained from the mass‐weighted average of the NR‐PM BC species) was associated with rBC. The peak in the average size distribution of the rBC‐containing particles measured by the SP‐AMS in vacuum aerodynamic diameter ( d va ) varied from ~100 nm to ~450 nm d va , with most of the rBC mass below 200 d va . The NR‐PM BC below 200 nm d va was primarily organic, whereas inorganics were generally found on larger rBC‐containing particles. Positive matrix factorization analyses of both SP‐AMS and HR‐AMS data identified organic aerosol factors that were correlated in time but had different fragmentation patterns due to the different instruments vaporization techniques. Finally, we provide an overview of the volatility properties of NR‐PM BC and report the presence of refractory oxygen species in some of the air masses encountered.
On the Ergodic Capacity of Frequency Selective MIMO Systems Equipped with MMSE Receivers: An Asymptotic Approach (2008)

This paper is devoted to the study of the ergodic capacity of frequency selective MIMO systems equipped with a MMSE receiver when the channel state information is available at the receiver side and when the second order statistics of the channel taps are known at the transmitter side. As the expression of this capacity is rather complicated and difficult to analyse, it is studied in the case where the number of transmit and receive antennas converge to +oo at the same rate. In this asymptotic regime, the main results of the paper are related to the design of an optimal precoder in the case where the transmit antennas are correlated. It is shown that the left singular eigenvectors of the optimum precoder coincide with the eigenvectors of the mean of the channel taps transmit covariance matrices, and its singular values are solution of a certain maximization problem.
Nonlinear optical properties of textured strontium barium niobate thin films prepared by metalorganic chemical vapor deposition (1995)

Highly textured strontium barium niobate thin films were deposited in situ by low pressure metalorganic chemical vapor deposition. [001]-oriented strontium barium niobate films on single crystal (100) magnesium oxide substrates were obtained at a growth temperature of 800 °C. Second-harmonic generation of 1.064 μm incident light was measured on the thin films. The nonlinear optical susceptibility of the films was as high as 8.7 times that of quartz (∼3.0 pm/V), which is comparable to the bulk value.
Dynamic Performance Optimization of a Pilot-Scale Reactive Distillation Process by Economics Optimizing Control (2018)

The most prominent example of process intensification by process integration is reactive distillation (RD), which can realize a high reactant conversion and a high purity of the target product in equilibrium-limited reaction systems. Reactive distillation is mostly used for single reactions, but realizations for multiple-reaction systems leading to more than one target product can also be found. In multipurpose chemical processes, the target product of a multiple-reaction system can be switched during the production. When combining fluid separation and multiple-reaction systems, e.g., in a RD column, it is challenging to find operating conditions that lead to the most profitable operation of the process. Economics optimizing control where an economic objective is employed in a model-predictive control framework has the potential to drive the process to the economic optimum during operation based upon a process model and online measurements. However, so far only few applications of such advanced process control (APC) concepts to reactive distillation processes have been realized and these do not concern multiple-reaction systems. In this contribution, we describe the application of economics optimizing control to a multiproduct RD process. The selected case study is a homogeneously catalyzed two-step transesterification reaction that is performed in a RD column in pilot-plant scale.
Optical Molecular Sensing in Complex Biological Environments (2014)

Although techniques in molecular imaging have advanced considerably over the past several decades, there remain numerous categories of biological molecular targets that are refractory to straightforward imaging. Among these is molecular oxygen, which is vital to a host of physiological as well as pathological processes, as well as the amorphous pigment pheomelanin, which may play a formerly unappreciated role in melanoma carcinogenesis.\n\nThis thesis describes two related bodies of work that advance techniques in oxygen and pheomelanin imaging, respectively. First, inspired by a desire to understand how hypoxia affects cancer chemotherapy on a cellular level, we designed and synthesized a novel oxygen-sensitive, dendritic nanoconstruct that is capable of spontaneously penetrating through hundreds of microns of multiple cellular layers. After demonstrating our nanoconjugate's oxygen sensitivity using time-domain phosphorescence lifetime measurements, we demonstrate that it retains its oxygen sensitivity in a 3D spheroid in vitro model of ovarian cancer through the use of a custom-made, near infrared-optimized confocal phosphorescence imaging system. Drawing from this approach, we then describe the fabrication and calibration of a separate oxygen-sensing bandage platform for use in wound-healing applications, and demonstrate its use in ex vivo and in vivo animal systems.\n\nThe second body of work describes the use of non-linear four-wave mixing techniques to facilitate straightforward imaging of the molecular pigment pheomelanin. Recent findings suggest that pheomelanin may play a previously unappreciated role in melanoma carcinogenesis, even in the complete absence of an ultraviolet light insult. However, due to its pale color, pheomelanin is difficult to visualize against a skin background, making its study challenging. After constructing a femtosecond-pulsed coherent anti-Stokes Raman scatter (CARS) microscopy imaging system, we use imaging and spectroscopy to provide proof-of-concept that pheomelanin can be imaged through a combination of CARS microscopy and electronically-enhanced four-wave mixing. We then use our non-linear imaging system to specifically observe pheomelanin in isolated "redhead" mouse melanocytes, and show through an siRNA gene knock-down strategy that our system can be used to observe changes in pheomelanin signal upon modification of biological pathways known to affect pheomelanin synthesis.
Stabilization in Strength of Hot-rolled Sheet Steel Strengthened by Nanometer-sized Carbides (2007)

Stable precipitation-strength of hot-rolled sheet steel can be realized with precipitates remaining fine even at high temperature coiling. This study deals with a relationship between the strength of ferritic steels strengthened by nanometer-sized carbides and coiling temperature in order to evaluate the stability of the strength against a deviation of coiling temperature. Ti-Mo-bearing and Ti-bearing steels were heat-treated for the precipitation of (Ti, Mo)C and TiC in ferrite matrix, respectively. These steels were hot-rolled and coiled in the temperature range from 550°C to 700°C. Matrix of the steels coiled at temperatures more than 600°C was only ferrite and nanometer-sized carbides in law were generated in the matrix. Ti-Mo-bearing steel exhibited high strength even at the high coiling temperature while the strength of Ti-bearing steel significantly decreased. Hardness of Ti-bearing steel just transformed at 650°C was the same as that at 625°C. In addition, while hardness of Ti-bearing steel coiled at 625°C significantly decreased during holding at 650°C for 86.4 ks, Ti-Mo-bearing steel did not show a large change in hardness. These results confirm that (Ti, Mo)C is not coarsened easily by Ostwald ripening at the high coiling temperature unlike TiC. Interfacial energy between (Ti, Mo)C and ferrite matrix can be the same as that in case of TiC since both carbides have the same structure and the equivalent lattice parameter. The retardation of Ostwald ripening of (Ti, Mo)C is attributed to a small amount of titanium in solution in Ti-Mo-bearing steel.
28-Gb/s 16-QAM OFDM Radio-over-Fiber System Within 7-GHz License-Free Band at 60 GHz Employing All-Optical Up-conversion (2009)

A record 28-Gb/s 16-QAM OFDM system within 7-GHz license-free band at 60 GHz employing all-optical up-conversion with frequency quintupling is experimentally demonstrated. Negligible penalty is observed following 100-km SMF transmission without any dispersion compensation.
Cutting Edge: Enhanced Anti-HIV-1 Activity and Altered Chemotactic Potency of NH2-Terminally Processed Macrophage-Derived Chemokine (MDC) Imply an Additional MDC Receptor (1998)

Abstract Posttranslational processing of chemokines increases (IL-8) or decreases (monocyte chemotactic protein-1) their chemotactic potency. Macrophage-derived chemokine (MDC) attracts monocytes, dendritic cells, activated lymphocytes, and NK cells and has reportedly anti-HIV-1 activity. Here we report that truncation of MDC by deletion of two NH2-terminal residues resulted in impaired binding to CC chemokine receptor (CCR)4, the only identified MDC receptor sofar. Truncated MDC(3-69) failed to desensitize calcium mobilization by MDC(1-69) or thymus- and activation-regulated chemokine (TARC), another CCR4 ligand. MDC(3-69) lacked HUT-78 T cell chemotactic activity but retained its capacity to attract monocytes and to desensitize chemotaxis. Compared with MDC(1-69), MDC(3-69) had weak but enhanced antiviral activity against M- and T-tropic HIV-1 strains. Furthermore, both MDC forms failed to signal through the orphan receptors Bonzo/STRL33 and BOB/GPR15 and to desensitize RANTES and stromal cell-derived factor (SDF)-1 responses in CCR5-transfected and CXC chemokine receptor (CXCR)4-transfected cells, respectively. These findings suggest that MDC recognizes another, yet unidentified, receptor. We conclude that minimal NH2-terminal truncation of MDC differentially affects its various immunologic functions.
General Catalysts for the Suzuki–Miyaura and Sonogashira Coupling Reactions of Aryl Chlorides and for the Coupling of Challenging Substrate Combinations in Water (2005)

Amphiphile Phosphanliganden (siehe Strukturen) lieferten bei palladiumkatalysierten Suzuki-Miyaura- und Sonogashira-Kupplungen in Wasser oder Zweiphasensystemen aus Wasser und einem organischen Solvens ausgezeichnete Ausbeuten an funktionalisierten Biarylen bzw. Arylalkinen.
Lithium-containing scintillators for thermal neutron, fast neutron, and gamma detection (2023)

In one embodiment, a scintillator includes a scintillator material; a primary fluor, and a Li-containing compound, where the Li-containing compound is soluble in the primary fluor, and where the scintillator exhibits an optical response signature for thermal neutrons that is different than an optical response signature for fast neutrons and gamma rays.
The succinct synthesis of AT13387, a clinically relevant Hsp90 inhibitor (2019)

AT13387 is an orally bioavailable clinical candidate developed to inhibit theheat shock protein 90 (Hsp90). This article describes a modified synthetic route for the multi-gram production of AT13387 in 46% overall yield. The modified synthetic route is short, avoids stringent reaction conditions and difficult purifications, which led to increase in an overall yield.