gebhart/patrepeval huggingface dataset:
Evidence for biosurfactant-induced flow in corners and bacterial spreading in unsaturated porous media (2021)

The spread of pathogenic bacteria in unsaturated porous media, where air and liquid coexist in pore spaces, is the major cause of soil contamination by pathogens, soft rot in plants, food spoilage, and many pulmonary diseases. However, visualization and fundamental understanding of bacterial transport in unsaturated porous media are currently lacking, limiting the ability to address the above contamination- and disease-related issues. Here, we demonstrate a previously unreported mechanism by which bacterial cells are transported in unsaturated porous media. We discover that surfactant-producing bacteria can generate flows along corners through surfactant production that changes the wettability of the solid surface. The corner flow velocity is on the order of several millimeters per hour, which is the same order of magnitude as bacterial swarming, one of the fastest known modes of bacterial surface translocation. We successfully predict the critical corner angle for bacterial corner flow to occur based on the biosurfactant-induced change in the contact angle of the bacterial solution on the solid surface. Furthermore, we demonstrate that bacteria can indeed spread by producing biosurfactants in a model soil, which consists of packed angular grains. In addition, we demonstrate that bacterial corner flow is controlled by quorum sensing, the cell-cell communication process that regulates biosurfactant production. Understanding this previously unappreciated bacterial transport mechanism will enable more accurate predictions of bacterial spreading in soil and other unsaturated porous media.
A 77 GHz CMOS power amplifier module using multi-layered redistribution layer technology (2013)

This paper presents a new millimeter-wave module concept, which is an integration of CMOS monolithic microwave integrated circuits (MMICs) and passive devices fabricated using a redistribution layer (RDL) technology. To realize a low-loss passive circuit, we introduced a multi-metal-layer for the RDL. The first metal layer was used as ground to shield from substrates. The upper metal layers form passive RF components such as a thin film microstrip line (TFMSL), a spiral inductor, a balun, a power combiner, and an antenna. Detailed measurements and characterizations are presented, and we show their applicability in the millimeter-wave region. Moreover, this concept was applied to an integrating millimeter-wave module consisting of four identical CMOS power amplifiers and RDL power combiners to increase the output power. The module exhibited a saturation power of 15 dBm, which is almost four-times higher than that obtained from the single PA. The measured small-signal gain of the PA module was 5.4 dB. The total chip size was 2.2 × 1.5 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The power consumption of the PA module was 800 mW.
Synthesis, biodistribution, and imaging of 68Ga-DTPA-BP in normal and bone metastasis rodent models (2008)

1233 Objectives: This study was aimed to develop 68Ga-N6-carboxymethyl-N3,N9-bis[[2,2-bis(phosphono)-2-hydroxy]ethyl]-3,6,9-triazaundecanedioic acid (DTPA-BP) for the detection of bone metastases by PET. Methods: DTPA-BP was synthesized by reacting tris(trimethylsilyl)phosphite with DTPA anhydride in THF. After solvent evaporation and methanolic hydrolysis, the product was purified from a sephadex-packed column. 68GaCL3 was eluted from a 68Ge/68Ga generator (Eckert & Ziegler, Berlin, Germany). DTPA-BP was labeled with 68Ga(III) using acetate buffer (PH 5). First, the biodistribution of 68Ga-DTPA-BP and 99mTc-MDP (reference standard) was studied in normal female F-344 rats at 0.5-2hrs by tissue sampling and gamma spectrometry. Then, the osteolytic bone metastases model was created by injecting PC-3 human prostate cancer cells into the left tibia of male SCID mice. PET-imaging of 68Ga-DTPA and 68Ga-DTPA-BP was performed in a microPET R4 (Siemens) at 0.5-2h post iv injection (150uCi/mouse). The specific activity of 68Ga-DTPA-BP was 75 Ci/mol. Results: The total synthesis yield of DTPA-BP was 10-15%. To achieve 80-90% radiochemical purity of 68Ga -DTPA-BP, the physical amount DTPA-BP was >1mM. The biodistribution of 68Ga-DTPA-BP in normal rats at 0.5-2 hrs post-injection revealed increased bone-to-blood (3.4+ 0.80 to 5.3+0.24) and bone-to-muscle (13.6+3.46 to 21.8+11.50) ratios. The uptake of 68Ga-DTPA-BP and 99mTc-MDP in bones at 0.5 hr was 2.2+0.45 and 3.9+0.31 %ID/g, respectively. PET with 68Ga-DTPA-BP was able to detect osteolytic bone metastases, but not with 68Ga-DTPA. Conclusions: 68Ga-DTPA-BP can detect osteolytic bone metastases. Further characterization of this novel tracer in different tumor models is underway.
Multivalent Peptide and Protein Dendrimers Using Native Chemical Ligation (2005)

A wide variety of well-defined multivalent peptides and proteins can be made by conjugating synthetic peptides and recombinantly expressed proteins to cysteine-functionalized dendrimers using native chemical ligation (see picture). This modular approach provides access to dendrimers that are attractive both for understanding fundamental issues of multivalency in biological interactions as well as for biomedical applications. Supporting information (synthesis and characterization of the dendrimers, including mass spectra for all the peptide and protein dendrimers) for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z500635_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Carrierless design for handling and processing of ultrathin wafers (2010)

A common requirement for all current and future TSV (Through Silicon Via) applications is the ability to handle and process thinned Silicon Wafers, usually in the range of 150μm or much below. Silicon Wafers of this thickness cannot be handled without support as wafers with the standard thickness. One solution to tackle this problem is the use of wafer-support-systems (WSS), in which the thinned wafers are bonded temporarily to a carrier wafer, which gives the wafer mechanical stability. Another solution for handling are carrierless systems, in which the wafer is modified in a way that it is thin and mechanically rigid at the same time. Existing carrierless systems provide mechanical integrity for the wafer, but lack the full integration into backside processing. In this paper, we present a carrierless approach that provides mechanical stability and can be integrated into backside processing technology at the same time. We present results of a carrierless wafer with a thickness of 60μm only which has undergone a bumping process at the backside.
Preclinical Screening of Splice-Switching Antisense Oligonucleotides in PDAC Organoids (2023)

Aberrant alternative splicing is emerging as a cancer hallmark and a potential therapeutic target. It is the result of dysregulated splicing factors or genetic alterations in splicing-regulatory <i>cis</i> -elements. Targeting individual altered splicing events associated with cancer-cell dependencies is a potential therapeutic strategy, but several technical limitations need to be addressed. Patient-derived organoids (PDOs) are a promising platform to recapitulate key aspects of disease states and to facilitate drug development for precision medicine. Here, we report an efficient antisense-oligonucleotide (ASO) transfection method to systematically evaluate and screen individual splicing events as therapeutic targets in pancreatic ductal adenocarcinoma (PDAC) organoids. This optimized delivery method allows fast and efficient screening of ASOs that reverse oncogenic alternative splicing. In combination with advancements in chemical modifications and ASO-delivery strategies, this method has the potential to accelerate the discovery of anti-tumor ASO drugs that target pathological alternative splicing.
Density relaxation in a vibrated granular material (1995)

We report measurements of the density of a vibrated granular material as a function of time. The material studied consists of monodisperse spherical glass particles confined to a long, thin cylindrical tube. Vibrations cause the pile to evolve from a low density initial configuration toward a steady state with a final density that depends on the intensity of the vibrations. We find a complex time evolution that is incompatible with a single exponential relaxation. There appears to be a characteristic value of the acceleration that separates two regimes of packing behavior. The results are compared to current theories of compaction.
Aryl Hydrocarbon Receptor-Interacting Protein Gene Mutations in Familial Isolated Pituitary Adenomas: Analysis in 73 Families (2007)

AIP mutations, of which nine new mutations have been described here, occur in approximately 15% of FIPA families. Although pituitary tumors occurring in association with AIP mutations are predominantly somatotropinomas, other tumor types are also seen. Further study of the impact of AIP mutations on protein expression and activity is necessary to elucidate their role in pituitary tumorigenesis in FIPA.
Cover Picture: Dual Unnatural Amino Acid Incorporation and Click‐Chemistry Labeling to Enable Single‐Molecule FRET Studies of p97 Folding (ChemBioChem 11/2016) (2016)

The cover picture shows a general labeling scheme used to create a dual-fluorophore labeled variant of a large cellular protein machine, p97, for folding studies. Dual unnatural amino acid incorporation was used to install azide moieties on the protein, which were subsequently used for site-specific dye labeling by using bioorthogonal Click-chemistry in a background of a large number of native cysteines. The scheme potentiates detailed biophysical studies of this and other large cellular proteins using single-molecule Förster resonance energy transfer (FRET). More information can be found in the communication by E. Chapman, A.A. Deniz et al. on page 981 in Issue 11, 2016 (DOI: 10.1002/cbic.201500695).
P‐168: Enhancing Efficiency of Light Emitting Devices by Using Dewetting Metallic Thin Film (2009)

Abstract Metallic Ag and Au nanostructures with different size on ITO coated glass substrates have been fabricated by using metal thin film dewetting technique for studying the light guide in a display system. The external quantum efficiency of the LED is influenced by high refracting rate materials. The increase of extraction efficiency is based on scattering light from the trapped photons. with Ag nanostructures in peripheral area of emitting region on the ITO coated glass substrates, the external quantum efficiency of devices increases by about 20 %. We have demonstrated that metal thin film dewetting technique can be applied to fabricate metallic nanostructures in backlight layer for LED or OLED systems.
CFO estimation algorithm for OQAM-OFDM systems based on the conjugate symmetry property (2012)

In this contribution, a carrier frequency offset (CFO) estimator for OQAM-OFDM systems based on the conjugate symmetry property of a properly designed synchronization sequence is proposed. It extends the concept of a previously described symbol-timing and phase offset recovery scheme to build a complete time-domain synchronization method. The outcome of numerical evaluations shows that the proposed CFO estimation algorithm is suitable as a coarse CFO correction for continuous stream transmission systems. It delivers satisfying results in case of AWGN channels as well as for channels with moderate delay spreads while exhibiting the drawback of a high sensitivity to symbol timing errors. Furthermore, the possibility to reduce the overhead of the synchronization sequence by allowing a certain amount of self-interference is investigated.
CHARACTERIZATION OF MAGNETIC NANOPARTICLE-EMBEDDED SU8 FOR MICROACTUATION (2008)

SU8 polymer with embedded magnetic nickel nanoparticles (SU8-Ni) can be used as a structural material for microsystems and has the potential to be used for biomedical applications where remote actuation is needed. A composition of SU8-Ni (12.5% Ni nanoparticles and 87.5% SU8-2010 by weight) is investigated in this paper. Polysilicon torsional actuators were fabricated to measure the saturation magnetic moment of the material, and measurements were validated with alternating gradient magnetometry (AGM). Optical transmittance of the magnetic polymer was measured with a spectrophotometer and compared to standard SU8-2010.
Physiological Numbers of CD4+ T Cells Generate Weak Recall Responses Following Influenza Virus Challenge (2010)

Naive and recall CD4(+) T cell responses were probed with recombinant influenza A viruses incorporating the OVA OT-II peptide. The extent of OT-II-specific CD4(+) T cell expansion was greater following primary exposure, with secondary challenge achieving no significant increase in numbers, despite higher precursor frequencies. Adoptive transfer experiments with OT-II TCR-transgenic T cells established that the predominant memory set is CD62L(hi), whereas the CD62L(lo) precursors make little contribution to the recall response. Unlike the situation described by other investigators, in which the transfer of very large numbers of in vitro-activated CD4 effectors can modify the disease process, providing CD62L(hi) or CD62L(lo) OT-II-specific T cells at physiological levels neither enhanced virus clearance nor altered clinical progression. Some confounding effects of the transgenic model were observed, with decreasing primary expansion efficiency correlating with greater numbers of transferred cells. This was associated with increased levels of mRNA for the proapoptotic molecule Bim in cells recovered following high-dose transfer. However, even with very low numbers of transferred cells, memory T cells did not expand significantly following secondary challenge. A similar result was recorded in mice primed and boosted to respond to an endogenous IA(b)-restricted epitope derived from the influenza virus hemagglutinin glycoprotein. Depletion of CD8(+) T cells during secondary challenge generated an increased accumulation of OT-II-specific T cells but only at the site of infection. Taken together, significant expansion was not a feature of these secondary influenza-specific CD4 T cell responses and the recall of memory did not enhance recovery.
Effects of Ni Addition on Sulfide Stress Cracking Resistance of Low Alloy Tempered Martensite Steels. (1994)

The detrimental effect of Ni addition on sulfide stress cracking (SSC) resistance has been well known since the beginning of the study on SSC. However, effects of Ni itself and untempered martensite which can be typically formed for Ni bearing steel have not been clearly established, In this paper, the effects of Ni addition on SSC resistance are investigated using constant load tests and DCB tests for low alloy tempered martensite steels. SSC threshold stress (a*h) decreases with an increase in Ni content at a constant yield strength. This is probably caused by the fact that fissures work as initiation sites of SSC.Onthe other hand, an addition of Ni raises slightly the value of Kjssc Each Klssc value is supposedto be determined by the hydrogen content. Hydrogen content when crack propagation stops decreases with an increase in Ni content, while hydrogen content increases with an increase in Ni content when the steel starts being exposed to a sour environment. Untemperedmartensite is formed during tempering at a temperature just below A.+. Steels with untempered martensite show lower values of ath and Klssc than those without untemperedmartensite at a constant yield strength. So an addition of Ni promotes the formation of fissures and accelerates SSC initiation even without untempered martensite. Furthermore, untempered martensite decreases even more SSC resistance.
On node and route choice models for high-dimensional road networks. (2016)

This paper discusses first order node models for macroscopic multi-commodity traffic simulation. There are two parts: (1) input-output flow computation based on input demand, input link priorities, split ratios that define how incoming flow is distributed between output links, and output supply; and (2) a traffic assignment algorithm for the case when split ratios are not known a priori or are only partially known. 
Input link priorities define how output supply is distributed between incoming flows. We deal with arbitrary input link priorities. Also, in this node model we specifically address the issue of the First-In-First-Out (FIFO) rule: in the case of one of the output links being overly congested the FIFO rule may be too restrictive, blocking the flow to other outputs and causing unreasonable spillback. We relax the FIFO rule through a parametrization that describes how output links influence each other and allows tuning the model to anything between full FIFO and no FIFO. 
In the existing research the prevailing approach to local traffic assignment is to use a mode choice (logit or probit) model. In this paper we discuss the shortcomings of the logit model and introduce a nonparametric route choice algorithm that produces split ratios based only on link demands and supplies. 
All methods in this paper are presented for multi-commodity traffic flows.
GaN Laser Diode Technology for Visible-Light Communications (2022)

Gallium nitride (GaN) laser diodes (LDs) are considered for visible light communications (VLC) in free space, underwater, and in plastic optical fibers (POFs). A review of recent results is presented, showing high-frequency operation of AlGaInN laser diodes with data transmission rates up to 2.5 Gbit/s in free space and underwater and high bandwidths of up to 1.38 GHz through 10 m of plastic optical fiber. Distributed feedback (DFB) GaN LDs are fabricated to achieve single-frequency operation. We report on single-wavelength emissions of GaN DFB LDs with a side-mode suppression ratio (SMSR) in excess of 35 dB.
Synchronized physiological monitoring using a distributed wireless intelligent sensor system (2004)

Psychophysiological evaluation of a group of subjects requires synchronized monitoring of the individual subjects in the group during collective events. We present a concept of a wireless distributed data acquisition system for prolonged, synchronized health/stress monitoring of a selected group of subjects. The wireless distributed data acquisition system uses wireless intelligent sensors (WHRM) as individual heart rate variability (HRV) monitors, and a mobile wireless gateway (MOGUL). Each microcontroller sensor is equipped with a low power/low range (up to 100 ft) wireless transceiver, and communicates with the mobile gateway whenever the gateway comes into a range and identifies itself. The system is used for stress level evaluation using HRV monitoring during intense military training, and could be used to evaluate the stress level of individuals within the group in different settings, such as battlefield monitoring or day-trading on the stock market. In this paper we present the implemented distributed system architecture, system design issues, and lessons learned during implementation of the system.
Impact of oilseed rape expressing the insecticidal cysteine protease inhibitor oryzacystatin on the beneficial predator Harmonia axyridis (multicoloured Asian ladybeetle) (2003)

Insect-resistant transgenic plants have been suggested to have deleterious effects on beneficial predators through transmission of the transgene product by the pest to the predator. To test this hypothesis, effects of oilseed rape expressing the cysteine protease inhibitor oryzacystatin-1 (OC-1) on the predatory ladybird Harmonia axyridis were investigated using diamondback moth Plutella xylostella as the pest species. As expected, oilseed rape expressing OC-1 had no effects on either development or survival of the pest, which utilizes serine digestive proteases. Immunoassays confirmed accumulation of the transgene product in pest larval tissues at levels of up to 3 ng per gut. Characterization of proteolytic digestive enzymes of H. axyridis demonstrated that larvae and adults utilize cysteine and aspartic proteases; the former activity was completely inhibited by oryzacystatin in vitro. However, when H. axyridis larvae consumed prey reared on OC-1 expressing plants over their entire life cycle, no significant effects upon survival or overall development were observed. The inhibitor initially stimulated development, with a shortening of the developmental period of the second instar by 27% (P < 0.0001) accompanied by a 36% increase in weight of second instar larvae (P = 0.007). OC-1 had no detrimental effects on reproductive fitness of adult H. axyridis. Interestingly there was a significant increase in consumption of OC-1 dosed prey. The results show that prey reared on transgenic plants expressing a protein which inhibited ladybird digestive enzymes in vitro had no effects in vivo; the ladybird was able to up-regulate digestive proteases in response to the inhibitor.
Effects of Terminal Sterilization on PEG‐Based Bioresorbable Polymers Used in Biomedical Applications (2016)

The effects of ethylene oxide (EO), vaporized hydrogen peroxide (VHP), gamma (γ) radiation, and electron-beam (E-beam) on the physiochemical and morphological properties of medical device polymers are investigated. Polymers with ether, carbonate, carboxylic acid, amide and ester functionalities are selected from a family of poly(ethylene glycol) (PEG) containing tyrosine-derived polycarbonates (TyrPCs) to include slow, medium, fast, and ultrafast degrading polymers. Poly(lactic acid) (PLA) is used for comparison. Molecular weight (<i>M</i><sub>w</sub>) of all tested polymers decreases upon gamma and E-beam, and this effect becomes more pronounced at higher PEG content. Gamma sterilization increases the glass transition temperature of polymers with high PEG content. EO esterifies the carboxylic acid groups in desaminotyrosol-tyrosine (DT) and causes significant degradation. VHP causes hydroxylation of the phenyl ring, and hydrolytic degradation. This study signifies the importance of the chemical composition when selecting a sterilization method, and provides suggested conditions for each of the sterilization methods.
Effects of OPA1 mutations on mitochondrial morphology and apoptosis: Relevance to ADOA pathogenesis (2006)

To characterize the molecular links between type-1 autosomal dominant optic atrophy (ADOA) and OPA1 dysfunctions, the effects of pathogenic alleles of this dynamin on mitochondrial morphology and apoptosis were analyzed, either in fibroblasts from affected individuals, or in HeLa cells transfected with similar mutants. The alleles were missense substitutions in the GTPase domain (OPA1(G300E) and OPA1(R290Q)) or deletion of the GTPase effector domain (OPA1(Delta58)). Fragmentation of mitochondria and apoptosis increased in OPA1(R290Q) fibroblasts and in OPA1(G300E) transfected HeLa cells. OPA1(Delta58) did not influence mitochondrial morphology, but increased the sensitivity to staurosporine of fibroblasts. In these cells, the amount of OPA1 protein was half of that in control fibroblasts. We conclude that GTPase mutants exert a dominant negative effect by competing with wild-type alleles to integrate into fusion-competent complexes, whereas C-terminal truncated alleles act by haplo-insufficiency. We present a model where antagonistic fusion and fission forces maintain the mitochondrial network, within morphological limits that are compatible with cellular functions. In the retinal ganglion cells (RGCs) of patients suffering from type-1 ADOA, OPA1-driven fusion cannot adequately oppose fission, thereby rendering them more sensitive to apoptotic stimuli and eventually leading to optic nerve degeneration.