gebhart/patrepeval huggingface dataset:
TAK1-binding protein 1 is a pseudophosphatase (2006)

TAB1 [TAK1 (transforming growth factor-beta-activated kinase 1)-binding protein 1] is one of the regulatory subunits of TAK1, a protein kinase that lies at the head of three pro-inflammatory kinase cascades. In the current study we report the crystal structure of the N-terminal domain of TAB1. Surprisingly, TAB1 possesses a fold closely related to that of the PPM (Mg2+- or Mn2+-dependent protein phosphatase) family as demonstrated by the close structural similarity with protein phosphatase 2C alpha. However, we were unable to detect any phosphatase activity for TAB1 using a phosphopeptide or p-nitrophenyl phosphate as substrate. Although the overall protein phosphatase 2C alpha fold is conserved in TAB1, detailed structural analyses and mutagenesis studies show that several key residues required for dual metal-binding and catalysis are not present in TAB1, although binding of a single metal is supported by soaking experiments with manganese and isothermal titration calorimetry. Thus, it appears that TAB1 is a 'pseudophosphatase', possibly binding to and regulating accessibility of phosphorylated residues on substrates downstream of TAK1 or on the TAK1 complex itself.
Systemic Fluorescence Imaging of Zebrafish Glycans with Bioorthogonal Chemistry (2015)

Vertebrate glycans constitute a large, important, and dynamic set of post-translational modifications that are notoriously difficult to manipulate and image. Although the chemical reporter strategy has been used in conjunction with bioorthogonal chemistry to image the external glycosylation state of live zebrafish and detect tumor-associated glycans in mice, the ability to image glycans systemically within a live organism has remained elusive. Here, we report a method that combines the metabolic incorporation of a cyclooctyne-functionalized sialic acid derivative with a ligation reaction of a fluorogenic tetrazine, allowing for the imaging of sialylated glycoconjugates within live zebrafish embryos.
A lithographic and etching study on EUV contact hole patterning for stochastic process mitigation towards advanced device scaling (2022)

In the last years, the continuous efforts on the development of extreme ultraviolet lithography (EUVL) have allowed to push the lithographic performance of the EUV photoresists on the ASML NXE:3400 full field exposure tool, however, stochastic resist roughness, local critical dimension uniformity (LCDU) and pattern defectivity at nano-scale are still the major limiting factors of the lithographic process window of EUV resist when looking at sub-40nm pitches for both linespace (LS) and contact hole (CH) applications, especially in the low exposure dose regime [1]. To be effective during the lithographic EUV resist screening evaluation phase for such tight pitches, imec has implemented since 2018 [2] additional metrology analysis after resist development inspection (ADI) to further quick feedback on the quantification of nano-failures (nano-bridges, broken lines, merging or missing contacts) induced by a stochastic EUV patterning regime, and thus to improve the resist design at lithographic step in a faster manner. In this work, we have further extended the examination of the resist performance introducing additional metrology analysis after pattern transfer in a silicon nitride (SiN) substrate. We present the characterization results on 40nm and 36nm pitch staggered dense contact holes looking at both lithographic and etching knobs to mitigate the patterning process stochastic issues, confirming that the holistic litho-etch approach is an important and necessary step in the development path of EUV advanced patterning applications towards high volume manufacturing and high-NA EUV lithography.
Suppression of mode partition noise in a multiwavelength semiconductor laser through hybrid mode locking (2002)

We demonstrate the suppression of intensity fluctuations, which are known as mode partition noise, in a multiwavelength semiconductor laser by using a hybrid mode-locking scheme. The laser design incorporates a saturable absorber and a gain-modulated semiconductor optical amplifier, along with spectral filtering, in an external cavity to achieve multiwavelength hybrid mode locking. The mode-locked laser produces an error-free (pulse Q>13) 300-MHz optical pulse train in each of three wavelength channels.
(Invited) Surface Reactions of Electrolyte with LiNixCoyMnzO2 Cathodes for Lithium Ion Batteries (2020)

Layered metal oxides with high nickel content are commonly used cathode materials in commercial lithium ion batteries due to high capacity and lower cost resulting from higher nickel content and lower cobalt content. Cathodes with increased nickel content suffer from rapid capacity fade due to a combination of thickening of the anode solid electrolyte interphase (SEI) and impedance growth on the cathode after extended cycling. While transition metal catalyzed degradation of the anode SEI has been widely proposed as a primary source of capacity loss, we propose that a related acid induced degradation of the anode SEI also occurs.
Active Learning for Interactive Multimedia Retrieval Algorithms that employ feedback from users to guide the search process can provide relatively rapid and efficient results from large multimedia data collections. (2008)

As the first decade of the 21st century comes to a close, growth in multimedia delivery infrastructure and public demand for applications built on this backbone are converging like never before. The push towards reaching truly interactive multimedia technologies becomes stronger as our media consumption paradigms continue to change. In this paper, we will profile a technology leading the way in this revolution: active learning. Active learning is a strategy that helps alleviate challenges inherent in multimedia information re- trieval through user interaction. We will show how active learning is ideally suited for the multimedia information retrieval problem by giving an overview of the paradigm and component technologies used with special attention given to the application scenarios in which these technologies are useful. Finally, we give insight into the future of this growing field and how it fits into the larger context of multimedia information retrieval.
Optical low-coherence reflectometry for non-destructive testing of silicon micromachined devices (2016)

In recent years the development of silicon micromachining technologies has required more efforts in research to find non-contact measurement techniques for in-depth, non-destructive inspection of layered and microstructured samples. In this work, we apply a optical low-coherence reflectometry for in-plane and out-of-plane measurements aimed at detecting the optical path between hidden interfaces of several silicon devices with characteristic distance in the range 3 - 17 μm. The implemented configuration is based on a fiberoptic Michelson interferometer and it used infrared broadband radiation in the wavelength range of 1.2 - 1.7 μm, exhibiting a coherence length shorter than 2 μm. Out-of-plane measurements were performed to detect the optical pathlength of the main structural layers of a MEMS gyroscope. Moreover, in-plane measurements on vertical periodic silicon/air microstructures allowed us to detect the optical path among several silicon/air interfaces. Arrays with different spatial period were tested and the optical distance between hidden interfaces was obtained with high in-depth resolution. The results were in good agreement with the design parameters of the specific device. The proposed spot optical technique is a powerful and highly versatile diagnostic tool for non-destructive testing of silicon devices.
On the error performance bound of ordered statistics decoding of linear block codes (2016)

In this paper, a novel simplified statistical approach to evaluate the error performance bound of Ordered Statistics Decoding (OSD) of Linear Block Codes (LBC) is investigated. First, we propose a novel statistic which depicts the number of errors contained in the ordered received noisy codeword. Then, simplified expressions for the probability mass function and cumulative distribution function are derived exploiting the implicit statistical independence property of the samples of the received noisy codeword before reordering. Second, we incorporate the properties of this new statistic to derive the simplified error performance bound of the OSD algorithm for all order-I reprocessing. Finally, with the proposed approach, we obtain computationally simpler error performance bounds of the OSD than those proposed in literature for all length LBCs.
Effect of superlattice on light output power of InGaN‐based light‐emitting diodes fabricated on underlying GaN substrates with different dislocation densities (2016)

Abstract We evaluated the electrical properties of InGaN‐based light‐emitting diodes (LEDs) with a surperlattice (SL) layer just below the MQWs for forming V‐shaped pits (V‐pits) on underlying GaN substrates with different dislocation densities (DDs). The SL was effective for improving the EL intensity for all the LEDs with different DDs. However, the improvement ratio decreased with decreasing DD. The SL is effective for performance improvement of the LEDs with high DDs. (© 2015 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
ChemInform Abstract: An Olefin Metathesis Based Strategy for the Construction of the JKL, OPQ, and UVW Ring Systems of Maitotoxin. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Ultrasensitive DNA detection based on target-triggered rolling circle amplification and fluorescent poly(thymine)-templated copper nanoparticles (2018)

We describe a novel strategy for the ultrasensitive detection of target DNA based on rolling circle amplification (RCA) coupled with fluorescent poly(thymine)-templated copper nanoparticles (poly T-CuNPs). In the presence of target DNA, a padlock DNA probe that consists of two regions: a target DNA-specific region and a poly(adenine) region, is circularized by the ligation reaction, and the subsequent RCA reaction is promoted to generate long, concatemeric, single-stranded DNA (ssDNA) with a lot of repetitive poly T sequences. As a result, a large number of poly T-CuNPs are formed, exhibiting a highly fluorescent signal. However, in the absence of target DNA or in the presence of non-specific target DNA, the padlock DNA probe is not circularized and the subsequent RCA is not executed, leading to no production of fluorescent poly T-CuNPs. With this simple strategy, we successfully analyzed the target DNA with the ultralow detection limit of 7.79 aM, a value that is 3 or 7 orders of magnitude lower than those of previous RCA-based fluorescent DNA detection strategies. In addition, the developed system was demonstrated to selectively discriminate non-specific target DNAs with one-base mismatch, suggesting potential application in the accurate diagnosis of single nucleotide polymorphisms or mutations.
Substitutions in a Major Histocompatibility Complex Class II-Restricted Human Immunodeficiency Virus Type 1 gp120 Epitope Can Affect CD4+T-Helper-Cell Function (1998)

It has been suggested that the inability of the immune response to control human immunodeficiency virus type 1 (HIV-1) replication may be due, at least in part, to the capacity of this virus to escape from immune recognition through mutation. While there is increasing evidence for the importance of HIV-1-specific CD4+ T cells in containing HIV-1 spread in the infected individual, little is known about the consequences of HIV-1 mutation on virus-specific CD() T-cell function. The impact of HIV-1 sequence variation on CD4+ T-helper (Th)- cell function was assessed with a rhesus monkey model for immune recognition of the HIV-1 envelope (Env) glycoprotein. A series of HIV-1 Env(484-496) variant peptides were shown to retain the ability to bind to the appropriate rhesus monkey major histocompatibility complex class II DR molecule. Peptides bearing substitutions at position 490, however, failed to drive the proliferation or cytokine secretion of two well-characterized HXBc2 Env-specific rhesus monkey CD4+ Th-cell lines. Exogenous costimulation was ineffective in complementing the ability of the nonstimulatory peptides to induce [3H]thymidine incorporation by these cells. Finally, HIV-1 Env(484-496) variant peptides with substitutions at position 490 antagonized the HXBc2 Env peptide-induced proliferative response of the CD4+ Th-cell lines. Thus, HIV-1 variants appear to have the capacity to neutralize the function of virus-specific CD4+ T lymphocytes.
A case of steroid-dependent myeloid granulocytic sarcoma masquerading as Crohn’s disease (2011)

Small bowel tumors and Crohn's disease are common causes of small bowel obstruction. Early stage neoplasms can easily be mistaken for Crohn's disease. Therefore, thorough work-ups including imaging studies and endoscopic evaluation with biopsies are critical for accurate diagnosis. Here we report a case of an otherwise healthy female with progressive onset of multiple, recurrent obstructive symptoms secondary to terminal ileal narrowing who was referred for management of steroid-dependent Crohn's disease. After thorough evaluation, the diagnosis was revised to myeloid granulocytic sarcoma involving the terminal ileum. In this case, a delay in diagnosis can be detrimental for prognosis, as myeloid granulocytic sarcoma is highly predictive of underlying acute myeloid leukemia and needs urgent referral for chemotherapy and/or resection.
Challenges of Smart System Integration (2010)

As a result of the growing complexity and miniaturization of innovative products systems integration is becoming more and more important for scientific and technical development. The micro and nano system technologies as well as electronics are playing a key role in today's product development and industrial progress. They enable the integration of mechanical, electrical, optical, chemical, biological and other functions into a very small space with dimensions ranging from sub micrometers up to some millimeters. This paper presents three examples of MEMS sensors developed at Fraunhofer ENAS and Chemnitz University of Technology and the approaches for their integration into smart systems. The first one is an active radio frequency identification label for the monitoring of shock, inclination and temperature during transportation processes. A MEMS spectrometer and gyroscopes will be demonstrated. Special emphasis is given to MEMS /nanointegration.
Alternatives to Total Shoulder Arthroplasty in the Young Patient (2004)

Early arthritis of the glenohumeral joint represents a diagnostic and therapeutic challenge. Equally challenging is the presence of arthritis at any stage in the young or active patient since joint replacement may not be desirable, while nonoperative treatment may not provide sufficient pain relief. The common theme of all glenohumeral arthritides is one of progressive, irreversible osteoarticular destruction. Articular damage is usually accompanied by secondary involvement of the synovium, capsule, glenohumeral ligaments, and rotator cuff. Surgical intervention is predicated on the specific condition, stage of the disease, and condition of the periarticular tissues. The authors will discuss surgical alternatives including arthroscopic debridement, glenoidplasty, capsular release, synovectomy, corrective osteotomy, core decompression, and soft tissue interposition arthroplasty.
Timestamped Term Representation for Implementing Prolog. (1986)

As high-throughput approaches in biological and biomedical research are transforming the life sciences into information-driven disciplines, modern analytics platforms for big data have started to address the needs for efficient and systematic data analysis and interpretation. We observe that radiobiology is following this general trend, with -omics information providing unparalleled depth into the biomolecular mechanisms of radiation response-defined as systems radiobiology. We outline the design of computational frameworks and discuss the analysis of big data in low-dose ionizing radiation (LDIR) responses of the mammalian brain. Following successful examples and best practices of approaches for the analysis of big data in life sciences and health care, we present the needs and requirements for radiation research. Our goal is to raise awareness for the radiobiology community about the new technological possibilities that can capture complex information and execute data analytics on a large scale. The production of large data sets from genome-wide experiments (quantity) and the complexity of radiation research with multidimensional experimental designs (quality) will necessitate the adoption of latest information technologies. The main objective was to translate research results into applied clinical and epidemiological practice and understand the responses of biological tissues to LDIR to define new radiation protection policies. We envisage a future where multidisciplinary teams include data scientists, artificial intelligence experts, DevOps engineers, and of course radiation experts to fulfill the augmented needs of the radiobiology community, accelerate research, and devise new strategies.
The autotaxin-LPA2 GPCR axis is modulated by γ-irradiation and facilitates DNA damage repair (2015)

Abstract In this study we characterized the effects of radiation injury on the expression and function of the autotaxin (ATX)–LPA2 GPCR axis. In IEC-6 crypt cells and jejunum enteroids quantitative RT-PCR showed a time- and dose-dependent upregulation of lpa2 in response to γ-irradiation that was abolished by mutation of the NF-κB site in the lpa2 promoter or by inhibition of ATM/ATR kinases with CGK-733, suggesting that lpa2 is a DNA damage response gene upregulated by ATM via NF-κB. The resolution kinetics of the DNA damage marker γ-H2AX in LPA-treated IEC-6 cells exposed to γ-irradiation was accelerated compared to vehicle, whereas pharmacological inhibition of LPA2 delayed the resolution of γ-H2AX. In LPA2-reconstituted MEF cells lacking LPA1&3 the levels of γ-H2AX decreased rapidly, whereas in Vector MEF were high and remained sustained. Inhibition of ERK1&2 or PI3K/AKT signaling axis by pertussis toxin or the C311A/C314A/L351A mutation in the C-terminus of LPA2 abrogated the effect of LPA on DNA repair. LPA2 transcripts in Lin−Sca-1+c-Kit+ enriched for bone marrow stem cells were 27- and 5-fold higher than in common myeloid or lymphoid progenitors, respectively. Furthermore, after irradiation higher residual γ-H2AX levels were detected in the bone marrow or jejunum of irradiated LPA2-KO mice compared to WT mice. We found that γ-irradiation increases plasma ATX activity and LPA level that is in part due to the previously established radiation-induced upregulation of TNFα. These findings identify ATX and LPA2 as radiation-regulated genes that appear to play a physiological role in DNA repair.
Design principles for heterointerfacial alloying kinetics at metallic anodes in rechargeable batteries (2022)

How surface chemistry influences reactions occurring thereupon has been a long-standing question of broad scientific and technological interest. Here, we consider the relation between the surface chemistry at interfaces and the reversibility of electrochemical transformations at rechargeable battery electrodes. Using Zn as a model system, we report that a moderate strength of chemical interaction between the deposit and the substrate-neither too weak nor too strong-enables highest reversibility and stability of the plating/stripping redox processes. Focused ion beam and electron microscopy were used to directly probe the morphology, chemistry, and crystallography of heterointerfaces of distinct natures. Analogous to the empirical Sabatier principle for chemical heterogeneous catalysis, our findings arise from competing interfacial processes. Using full batteries with stringent negative electrode-to-positive electrode capacity (N:P) ratios, we show that such knowledge provides a powerful tool for designing key materials in highly reversible battery systems based on Earth-abundant, low-cost metals such as Zn and Na.
Spread of Terbinafine-Resistant Trichophyton mentagrophytes Type VIII (India) in Germany–“The Tip of the Iceberg?” (2020)

Chronic recalcitrant dermatophytoses, due to <i>Trichophyton</i> (<i>T</i>.) <i>mentagrophytes</i> Type VIII are on the rise in India and are noteworthy for their predominance. It would not be wrong to assume that travel and migration would be responsible for the spread of <i>T</i>. <i>mentagrophytes</i> Type VIII from India, with many strains resistant to terbinafine, to other parts of the world. From September 2016 until March 2020, a total of 29 strains of <i>T</i>. <i>mentagrophytes</i> Type VIII (India) were isolated. All patients were residents of Germany: 12 females, 15 males and the gender of the remaining two was not assignable. Patients originated from India (11), Pakistan (two), Bangladesh (one), Iraq (two), Bahrain (one), Libya (one) and other unspecified countries (10). At least two patients were German-born residents. Most samples (21) were collected in 2019 and 2020. All 29 <i>T</i>. <i>mentagrophytes</i> isolates were sequenced (internal transcribed spacer (ITS) and translation elongation factor 1-α gene (TEF1-α)). All were identified as genotype VIII (India) of <i>T</i>. <i>mentagrophytes</i>. In vitro resistance testing revealed 13/29 strains (45%) to be terbinafine-resistant with minimum inhibitory concentration (MIC) breakpoints ≥0.2 µg/mL. The remaining 16 strains (55%) were terbinafine-sensitive. Point mutation analysis revealed that 10/13 resistant strains exhibited Phe<sup>397</sup>Leu amino acid substitution of squalene epoxidase (SQLE), indicative for in vitro resistance to terbinafine. Two resistant strains showed combined Phe<sup>397</sup>Leu and Ala<sup>448</sup>Thr amino acid substitutions, and one strain a single Leu<sup>393</sup>Phe amino acid substitution. Out of 16 terbinafine-sensitive strains, in eight Ala<sup>448</sup>Thr, and in one Ala<sup>448</sup>Thr +, new Val<sup>444</sup> Ile amino acid substitutions were detected. Resistance to both itraconazole and voriconazole was observed in three out of 13 analyzed strains. Treatment included topical ciclopirox olamine plus topical miconazole or sertaconazole. Oral itraconazole 200 mg twice daily for four to eight weeks was found to be adequate. Terbinafine-resistant <i>T</i>. <i>mentagrophytes</i> Type VIII are being increasingly isolated. In Germany, transmission of <i>T</i>. <i>mentagrophytes</i> Type VIII from the Indian subcontinent to Europe should be viewed as a significant public health issue.
The influence of electron-hole separation on the recombination probability in photochromic glasses (1979)

Abstract It has previously been shown that the fading rate of photoehromic glasses depends on darkening conditions. A trapped-hole diffusion model was proposed to explain this effect (Araujo 1968, 1971). In this paper a temperature-dependent recombination term which decreases exponentially with electron-hole separation is included in the diffusion model. Peculiar low-temperature effects are predicted and these are observed in some photochromic glasses.