gebhart/patrepeval huggingface dataset:
Perinatal and Early-Life Nutrition, Epigenetics, and Allergy (2021)

Epidemiological studies have shown a dramatic increase in the incidence and the prevalence of allergic diseases over the last several decades. Environmental triggers including risk factors (e.g., pollution), the loss of rural living conditions (e.g., farming conditions), and nutritional status (e.g., maternal, breastfeeding) are considered major contributors to this increase. The influences of these environmental factors are thought to be mediated by epigenetic mechanisms which are heritable, reversible, and biologically relevant biochemical modifications of the chromatin carrying the genetic information without changing the nucleotide sequence of the genome. An important feature characterizing epigenetically-mediated processes is the existence of a time frame where the induced effects are the strongest and therefore most crucial. This period between conception, pregnancy, and the first years of life (e.g., first 1000 days) is considered the optimal time for environmental factors, such as nutrition, to exert their beneficial epigenetic effects. In the current review, we discussed the impact of the exposure to bacteria, viruses, parasites, fungal components, microbiome metabolites, and specific nutritional components (e.g., polyunsaturated fatty acids (PUFA), vitamins, plant- and animal-derived microRNAs, breast milk) on the epigenetic patterns related to allergic manifestations. We gave insight into the epigenetic signature of bioactive milk components and the effects of specific nutrition on neonatal T cell development. Several lines of evidence suggest that atypical metabolic reprogramming induced by extrinsic factors such as allergens, viruses, pollutants, diet, or microbiome might drive cellular metabolic dysfunctions and defective immune responses in allergic disease. Therefore, we described the current knowledge on the relationship between immunometabolism and allergy mediated by epigenetic mechanisms. The knowledge as presented will give insight into epigenetic changes and the potential of maternal and post-natal nutrition on the development of allergic disease.
Minimal complexity for the simplest protocol (1991)

The design issues of a multimedia transport protocol, TP5, which achieves the multiplexing of both real time and normal data flows at the transport layer are discussed. The use of a single transport connection to carry both data flows is proposed. Two schemes for the support of the synchronization of these data flows are presented. The protocol TP5 implementing the above mechanisms is described. It is shown that with the use of the described synchronization schemes, the TP5 protocol minimizes the control of the real time traffic while still controlling the normal data flow.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Hyperactivation is sufficient to release porcine sperm from immobilized oviduct glycans (2022)

Fertilizing sperm are retained by adhesion to specific glycans on the epithelium of the oviduct forming a reservoir before sperm are released from the reservoir so fertilization can ensue. Capacitated sperm lose affinity for the oviduct epithelium but the components of capacitation that are important for sperm release are uncertain. One important correlate of capacitation is the development of hyperactivated motility. Hyperactivation is characterized by asymmetrical flagellar beating with high beat amplitude. We tested whether the development of full-type asymmetrical motility was sufficient to release sperm from immobilized oviduct glycans. Sperm hyperactivation was induced by four different compounds, a cell-permeable cAMP analog (cBiMPS), CatSper activators (4-aminopyridine and procaine), and an endogenous steroid (progesterone). Using standard analysis (CASA) and direct visualization with high-speed video microscopy, we first confirmed that all four compounds induced hyperactivation. Subsequently, sperm were allowed to bind to immobilized oviduct glycans, and compounds or vehicle controls were added. All compounds caused sperm release from immobilized glycans, demonstrating that hyperactivation was sufficient to release sperm from oviduct cells and immobilized glycans. Pharmacological inhibition of the non-genomic progesterone receptor and CatSper diminished sperm release from oviduct glycans. Inhibition of the proteolytic activities of the ubiquitin-proteasome system (UPS), implicated in the regulation of sperm capacitation, diminished sperm release in response to all hyperactivation inducers. In summary, induction of sperm hyperactivation was sufficient to induce sperm release from immobilized oviduct glycans and release was dependent on CatSper and the UPS.
Controlling accesses to a branch prediction unit for sequences of fetch groups (2023)

An electronic device handles accesses of a branch prediction functional block when executing instructions in program code. The electronic device includes a processor having the branch prediction functional block that provides branch prediction information for control transfer instructions (CTIs) in the program code and a minimum predictor use (MPU) functional block. The MPU functional block determines, based on a record associated with a given fetch group of instructions, that a specified number of subsequent fetch groups of instructions that were previously determined to include no CTIs or conditional CTIs that were not taken are to be fetched for execution in sequence following the given fetch group. The MPU functional block then, when each of the specified number of the subsequent fetch groups is fetched and prepared for execution, prevents corresponding accesses of the branch prediction functional block for acquiring branch prediction information for instructions in that subsequent fetch group.
Platform Based Design of Termninals and Infrastructure Components for Cognitive Wireless Networks (2007)

Cooperation in wireless networks will facilitate a new dimension in the evolution of multimedia communications, sCtting out from the today's situation with a multitude of communication standards and radio interfaces both in the licensed and thC unlicensed domain. In order to pave the way towards cooperative networks, the deployment of cognitive wireless solutions, which will form the communication platforms, will be a key asset. In the future, we expect to see an increasingly flexible, ad-hoc utilization of the available spectrum in the unlicensed domain and a co-existence of communication standards in the licensed bands. In this communication, the authors will illustrate a platform based approach towards cognitive wireless communications. Also, the authors will present three software defined radio concepts designed by the members of the Lehrstuhl für KommunikationsTechnik, namely the HAWK (Highly Adaptable Wireless Kit), the FALCON (Flxible Access Logic for COmmunication Networks), and the MUSTANG (MUlti-STAndard single chip transceiver for the Next Generation), finally, giving an outlook on their wireless optical communication device, termed ARGOS. HAWK, FALCON, MUSTANG and ARGOS form the basis of the cognitive wireless platform, developed by the authors, termed PROMETHEUS. The setup of PROMETHEUS and its functionality shall be illustrated together with selected measurement results.
Synthesis and characterization of oligodeoxyribonucleotides containing terminal phosphates. NMR, UV spectroscopic and thermodynamic analysis of duplex formation of [d(pGGAATTCC)]2, [d(GGAATTCCp)]2and [d(pGGAATTCCp)]2 (1987)

Derivatives of the oligomer [d(GGAATTCC)]2 with 5' (5'-P), 3' (3'-P) and both 5' and 3' (5',3'-P2) terminal phosphate groups have been synthesized and studied by temperature dependent UV and NMR spectroscopic methods. Thermodynamic studies of the helix to strand transition indicate that addition of 3' phosphate groups has very little effect on the delta G degree for helix formation at 37 degrees C while addition of 5' phosphate groups adds approximately -0.5 kcal/mole to the delta G degree for duplex formation. The helix stabilization by 5' phosphate groups occurs at salt concentrations of 0.1 M and above, and is primarily enthalpic in origin. Tm studies as a function of ionic strength also indicate that the oligomers fall into two groups with the parent and 3'-P derivatives being similar but less stable than the 5'-P and 5',3'-P2 derivatives. Imino proton and 31P NMR studies also divide the oligomers into these same two groups based on spectral comparisons and temperature induced chemical shift and linewidth changes. 31P NMR analysis suggests that addition of 5' phosphate groups results in a small change in phosphodiester torsional angles in the g,t to g,g direction, indicating improved base stacking at the 5' end of the modified oligomer. No such changes are seen at the 3' end of the oligomer on adding 3' phosphate groups.
Association of Angiopoietin-2 and Ki-67 Expression with Vascular Density and Sunitinib Response in Metastatic Renal Cell Carcinoma (2016)

The Angiopoietin-2 (Ang2, Angpt2) growth factor is a context-dependent antagonist/agonist ligand of the endothelial Tie2 receptor tyrosine kinase and known to promote tumour angiogenesis and metastasis. Angiopoietin antagonists have been tested in clinical cancer trials in combination with VEGF-based anti-angiogenic therapy, including sunitinib, which is widely used as a first-line therapy for metastatic renal cell carcinoma (mRCC). However, little is known about Ang2 protein expression in human tumours and the correlation of tumour Ang2 expression with tumour vascularization, tumour cell proliferation and response to anti-angiogenic therapies. Here, we evaluated, using immunohistochemistry, the expression of Ang2, CD31 and the cell proliferation marker Ki-67 in the primary kidney cancer from 136 mRCC patients, who received first-line sunitinib after nephrectomy. Ang2 protein expression was restrained to RCC tumour vessels, and correlated with tumour vascularization and response to sunitinib. High pre-therapeutic Ang2 expression, and more strongly, combined high expression of both Ang2 and CD31, were associated with a high clinical benefit rate (CBR). Low cancer Ki-67 expression, but not Ang2 or CD31 expression, was associated with favourable progression-free (PFS) and overall survival (OS) as compared to patients with high Ki-67 expression (PFS 6.5 vs. 10.6 months, P = 0.009; OS, 15.7 vs. 28.5 months, P = 0.015). In summary, in this study to investigate endothelial Ang2 in mRCC patients treated with first-line sunitinib, high cancer Ang2 expression was associated with the CBR, but not PFS or OS, whereas low Ki-67 expression was significantly associated with long PFS and OS.
Preparation of 5-unsubstituted 4-formylpyrrole-2-carboxylates and conversion to cycloalkano-oligopyrroles † (2000)

Ethyl 4-formylpyrrole-2-carboxylates were prepared from nitroacetaldehyde dimethyl acetal in 9–50% yields using the Barton–Zard reaction. These formylpyrroles were successfully transformed to cycloalkano-oligopyrroles. The conformation of cyclononatripyrroles in CDCl3 was found to be a crown form based on the NMR analysis, while cyclododecatetrapyrroles were in two interconverting boat and chair conformations.
Harnessing Colon Chip Technology to Identify Commensal Bacteria That Promote Host Tolerance to Infection (2021)

Commensal bacteria within the gut microbiome contribute to development of host tolerance to infection, however, identifying specific microbes responsible for this response is difficult. Here we describe methods for developing microfluidic organ-on-a-chip models of small and large intestine lined with epithelial cells isolated from duodenal, jejunal, ileal, or colon organoids derived from wild type or transgenic mice. To focus on host-microbiome interactions, we carried out studies with the mouse Colon Chip and demonstrated that it can support co-culture with living gut microbiome and enable assessment of effects on epithelial adhesion, tight junctions, barrier function, mucus production, and cytokine release. Moreover, infection of the Colon Chips with the pathogenic bacterium, <i>Salmonella typhimurium</i>, resulted in epithelial detachment, decreased tight junction staining, and increased release of chemokines (CXCL1, CXCL2, and CCL20) that closely mimicked changes previously seen in mice. Symbiosis between microbiome bacteria and the intestinal epithelium was also recapitulated by populating Colon Chips with complex living mouse or human microbiome. By taking advantage of differences in the composition between complex microbiome samples cultured on each chip using 16s sequencing, we were able to identify <i>Enterococcus faecium</i> as a positive contributor to host tolerance, confirming past findings obtained in mouse experiments. Thus, mouse Intestine Chips may represent new experimental <i>in vitro</i> platforms for identifying particular bacterial strains that modulate host response to pathogens, as well as for investigating the cellular and molecular basis of host-microbe interactions.
A membrane-associated, carbohydrate-modified form of the v-abl protein that cannot be phosphorylated in vivo or in vitro (1984)

Abelson murine leukemia virus encodes a transforming protein which contains tyrosine kinase activity and is phosphorylated in vivo and in vitro. We found that P160 and P160-derived virus strains expressed an additional, altered v-abl protein which could not be phosphorylated. The altered v-abl protein (L-v-abl) differed from the phosphorylated form (K-v-abl) in that it was glycosylated and localized exclusively to the membrane fraction. Tunicamycin inhibition of N-linked carbohydrate addition did not restore phosphorylation. It did, however, reveal that L-v-abl had additional sequences relative to K-v-abl. The coding sequences required for this region and for the expression of L-v-abl were identified by replacing sequences in the P120 virus genome, which did not express L-v-abl, with sequences from the P160 virus genome. The necessary sequences were localized to the Moloney murine leukemia virus-derived gag gene. Comparison between the in vitro altered P120 and wild-type P120 virus strains indicated that expression of L-v-abl did not increase the efficiency of lymphoid transformation. Although the biological role of L-v-abl is not clear, our analyses have revealed that a specific amino terminal gag sequence can prevent v-abl from acting as a kinase substrate and can alter the cellular localization and modification of v-abl. These properties distinguish L-v-abl from previously reported v-abl proteins.
Dual Coating Improves the Survival of Probiotic Bifidobacterium Strains during Exposure to Simulated Gastro-Intestinal Conditions (2013)

프로바이오틱 박테리아는 면역력 활성 조절, 콜레스테롤 수치 억제, 유당내성 강화, 항종양 활성 등의 다양한 생리활성 기능으로 건강 증진 효과가 있는 것으로 보고되고 있다. 프로바이오틱 박테리아는 일단 섭취하게 되면 위장관을 통과하는 동안 산도가 낮거나 단백질분해 효소가 많은 열악한 환경에서 생존해야 하며 프로바이오틱 효과를 발휘하기 위해 증식해야 한다. 이중 코팅 기술은 펩타이드와 다당류의 이중코팅으로 섭취된 프로바이오틱 박테리아를 열악한 조건으로부터 보호하기 위해 개발되었다. 본 연구에서는 이중코팅 된 4종의 비피도박테리움 혼합물의 생존 안정성을 평가하기 위해 코팅이 되지 않은 비피도박테리움 혼합물과 담즙, 산 저항성 및 열 안정성을 비교 평가하였다. 이중 코팅 된 균주와 코팅이 되지 않은 균주를 산과 담즙 조건 및 <TEX>$40^{\circ}C$</TEX>에 노출 시킨 후 한천배지에 배양하여 생존생육 세포수를 측정하였으며, BacLigtht 키트를 이용하여 염색 한 후 유세포 분석기를 이용하여 생균과 사균의 세포수를 평가하였다. 이중코팅 된 균주 혼합물의 경우 코팅이 되지 않은 균주 혼합물 보다 산, 담즙 내성이 더 높았으며, 열 안전성 또한 코팅 되지 않은 균주 혼합물보다 높은 것으로 나타났다. 이 같은 결과들로 이중코팅 기술은 프로바이오틱 박테리아의 안정성 및 섭취 후 위장관 트랙을 통과하는 동안 균주의 생존률을 향상시킬 수 있음을 확인하였다. Probiotics have been reported to benefit human health by modulating immunity, lowering cholesterol, improving lactose tolerance, and preventing some cancer. Once ingested, probiotic microorganisms have to survive harsh conditions such as low pH, protease-rich condition, and bile salts during their passage through the gastro-intestinal (GI) tract colonize and proliferate to exert their probiotic effects. The dual coating technology, by which the bacteria are doubly coated with peptides and polysaccharides in consecutive order, was developed to protect the ingested bacteria from the harsh conditions. The aim of the study was to evaluate the viable stability of a doubly coated blend of four species of Bifidobacterium by comparing its bile/acid resistance and heat viability in vitro with that of the non-coated blend. After challenges with acid, bile salts, heat, and viable cell counts (VVCs) of the dual coated and non-coated blend were determined by cultivation on agar plates or flow cytometric measurement after being stain with the BacLigtht kit<TEX>$^{TM}$</TEX>. The results showed that the dual coated blend was much higher resistant to the acidic or bile salt condition than the non-coated blend and heat viability was also higher, indicating that the dual coating can improve the survival of probiotic bacteria during their transit through the GI tract after consumption.
The Complex Role of Multivalency in Nanoparticles Targeting the Transferrin Receptor for Cancer Therapies (2020)

Transferrin receptor (TfR, CD71) has long been therapeutic target due to its over-expression on many malignant tissues. In this study, PRINT® nanoparticles were conjugated with TfR ligands for targeted drug delivery. Cylindrical poly(ethylene glycol)-based PRINT nanoparticles (diameter [d] = 200 nm, height [h] = 200 nm) labeled with transferrin receptor antibody (NP-OKT9) or human transferrin (NP-hTf), showed highly specific TfR-mediated uptake by all human tumor cell lines tested, relative to negative controls (IgG1 for OKT9 or bovine transferrin (bTf) for hTf). The targeting efficiency was dependent on particle concentration, ligand density, dosing time and cell surface receptor expression level. Interestingly, NP-OKT9 or NP-hTf showed little cytotoxicity on all solid tumor cell lines tested but were very toxic to Ramos B-cell lymphoma, whereas free OKT9 or hTf was not toxic. There was a strong correlation between TfR ligand density on particle surface and cell viability and particle uptake. NP-OKT9 and NP-hTf were internalized into acidic intracellular compartments but were not localized in EEA1 enriched early endosomes or lysosomes. Elevated caspase 3/7 activity indicates activation of apoptosis pathways upon particle treatment. Supplementation of iron suppressed the toxicity of NP-OKT9 but not NP-hTf, suggesting different mechanisms by which NP-hTf and NP-OKT9 exerts cytotoxicity on Ramos cells. Based on such an observation, the complex role of multivalency in nanoparticles is discussed. In addition, our data clearly reveal that one must be careful in making claims of “lack of toxicity” when a targeting molecule is used on nanoparticles and also raise concerns for unanticipated off-target effects when one is designing targeted chemotherapy nano-delivery agents.
Spatiotemporal Bundle Adjustment for Dynamic 3D Human Reconstruction in the Wild (2020)

Bundle adjustment jointly optimizes camera intrinsics and extrinsics and 3D point triangulation to reconstruct a static scene. The triangulation constraint, however, is invalid for moving points captured in multiple unsynchronized videos and bundle adjustment is not designed to estimate the temporal alignment between cameras. We present a spatiotemporal bundle adjustment framework that jointly optimizes four coupled sub-problems: estimating camera intrinsics and extrinsics, triangulating static 3D points, as well as sub-frame temporal alignment between cameras and computing 3D trajectories of dynamic points. Key to our joint optimization is the careful integration of physics-based motion priors within the reconstruction pipeline, validated on a large motion capture corpus of human subjects. We devise an incremental reconstruction and alignment algorithm to strictly enforce the motion prior during the spatiotemporal bundle adjustment. This algorithm is further made more efficient by a divide and conquer scheme while still maintaining high accuracy. We apply this algorithm to reconstruct 3D motion trajectories of human bodies in dynamic events captured by multiple uncalibrated and unsynchronized video cameras in the wild. To make the reconstruction visually more interpretable, we fit a statistical 3D human body model to the asynchronous video streams.Compared to the baseline, the fitting significantly benefits from the proposed spatiotemporal bundle adjustment procedure. Because the videos are aligned with sub-frame precision, we reconstruct 3D motion at much higher temporal resolution than the input videos.
Dilute Alloys Based on Au, Ag, or Cu for Efficient Catalysis: From Synthesis to Active Sites (2022)

The development of new catalyst materials for energy-efficient chemical synthesis is critical as over 80% of industrial processes rely on catalysts, with many of the most energy-intensive processes specifically using heterogeneous catalysis. Catalytic performance is a complex interplay of phenomena involving temperature, pressure, gas composition, surface composition, and structure over multiple length and time scales. In response to this complexity, the integrated approach to heterogeneous dilute alloy catalysis reviewed here brings together materials synthesis, mechanistic surface chemistry, reaction kinetics, in situ and operando characterization, and theoretical calculations in a coordinated effort to develop design principles to predict and improve catalytic selectivity. Dilute alloy catalysts─in which isolated atoms or small ensembles of the minority metal on the host metal lead to enhanced reactivity while retaining selectivity─are particularly promising as selective catalysts. Several dilute alloy materials using Au, Ag, and Cu as the majority host element, including more recently introduced support-free nanoporous metals and oxide-supported nanoparticle "raspberry colloid templated (RCT)" materials, are reviewed for selective oxidation and hydrogenation reactions. Progress in understanding how such dilute alloy catalysts can be used to enhance selectivity of key synthetic reactions is reviewed, including quantitative scaling from model studies to catalytic conditions. The dynamic evolution of catalyst structure and composition studied in surface science and catalytic conditions and their relationship to catalytic function are also discussed, followed by advanced characterization and theoretical modeling that have been developed to determine the distribution of minority metal atoms at or near the surface. The integrated approach demonstrates the success of bridging the divide between fundamental knowledge and design of catalytic processes in complex catalytic systems, which can accelerate the development of new and efficient catalytic processes.
Development of a flexible end-shield using tungsten curtains for 3D PET (2005)

In the three-dimensional (3D) acquisition of positron emission tomograph (PET) without septa, random and scatter due to the events from the outside the field of view (FOV) become a serious problem. They decrease the signal to noise ratio and quantitation of the image. They also limit the count rate capability of the PET system. To reduce these effects, we developed an end-shield using tungsten curtains. The end-shield consists of a mobile stand, a cylindrical support, and flexible tungsten curtains. The tungsten curtains are made of 4 layers of 30 mm square, 1 mm thick tungsten plates contained in pockets of cloth. Because the tungsten curtains are flexible, it could be used quite safely even in the body studies. Reduction of random and scatter were observed by using the end-shield in both phantom and human studies. Results indicate that the new end-shield using tungsten curtains is promising to improve the image quality of the PET studies.