gebhart/patrepeval huggingface dataset:
Geometric Analysis of Shapes in Ion Mobility–Mass Spectrometry (2022)

Experimental ion mobility-mass spectrometry (IM-MS) results are often correlated to three-dimensional structures based on theoretical chemistry calculations. The bottleneck of this approach is the need for accurate values, both experimentally and theoretically predicted. Here, we continue the development of the trend-based analyses to extract structural information from experimental IM-MS data sets. The experimental collision cross-sections (CCSs) of synthetic systems such as homopolymers and small ionic clusters are investigated in terms of CCS trends as a function of the number of repetitive units (e.g., degree of polymerization (DP) for homopolymers) and for each detected charge state. Then, we computed the projected areas of expanding but perfectly defined geometric objects using an in-house software called MoShade. The shapes were modeled using computer-aided design software where we considered only geometric factors: no atoms, mass, chemical potentials, or interactions were taken into consideration to make the method orthogonal to classical methods for 3D shape assessments using time-consuming computational chemistry. Our modeled shape evolutions favorably compared to experimentally obtained CCS trends, meaning that the apparent volume or envelope of homogeneously distributed mass effectively modeled the ion-drift gas interactions as sampled by IM-MS. The CCSs of convex shapes could be directly related to their surface area. More importantly, this relationship seems to hold even for moderately concave shapes, such as those obtained by geometry-optimized structures of ions from conventional computational chemistry methods. Theoretical sets of expanding beads-on-a-string shapes allowed extracting accurate bead and string dimensions for two homopolymers, without modeling any chemical interactions.
Sulfonated Polyrotaxane Surfaces with Basic Fibroblast Growth Factor Alter the Osteogenic Potential of Human Mesenchymal Stem Cells in Short-Term Culture (2019)

Human mesenchymal stem cells (hMSCs) are prone to senescence and lose their differentiation potential when expanded under nonfavorable conditions. This leads to the underutilization of hMSCs in clinical situations such as bone regeneration. The use of growth factors and small molecules as supplements and changing the physical properties of the cell culture surface have been explored to maintain the self-renewal and differentiation potential of hMSCs during the in vitro expansion phase. Here, we have explored the effect of polyrotaxanes (PRXs) with different molecular mobilities along with either soluble or immobilized fibroblast growth factor 2 (FGF2) in the maintenance of the osteogenic differentiation potential of hMSCs during in vitro expansion. We found that a less expanded shape of the hMSCs was associated with highly mobile PRX surfaces, and less mobile PRX surfaces led to flattened cell morphology. The presence of FGF2 induced further expansion of the cell shape and size. The immobilization of FGF2 helped to improve the yield of hMSCs on highly mobile surfaces by promoting cell attachment to the surfaces. hMSCs cultured on highly mobile PRX surfaces exhibited poor actin cytoskeletal organization and retention of the transcriptional regulator, yes-associated protein (YAP), in cytoplasm in contrast to the hMSCs on less mobile PRX surfaces. When the hMSCs that proliferated under these conditions were collected and subjected to osteogenic differentiation on tissue culture polystyrene (TCPS) surfaces, we found that only the hMSCs cultured on highly mobile PRXs with FGF2 in both soluble and immobilized forms showed mineralization indicative of osteogenic differentiation. Further, we found that hMSCs cultured on highly mobile PRX surfaces expressed higher levels of stemness marker genes, <i>Nanog</i> and <i>Oct4</i>. These results indicate that culturing hMSCs on PRX surfaces with different molecular mobilities even for a short period of time (4 days) was sufficient to cause a drastic change in the osteogenic potential. From these results, it is suggested that apart from the use of supplements such as FGF2 in its freely soluble or immobilized form, the consideration of proper molecular mobility of the substrates could enable us to design better culture conditions for the hMSCs with osteogenic potential.
Generation of pulsed-correlated photon pairs in the 1550nm band using a PPLN waveguide (2004)

We report a generation of pulsed correlated photon pairs in the 1550 nm band which is essential to long-distance fiber-optic quantum information and communication. We performed two-photon interference experiments using a Mach-Zehnder interferometer to demonstrate the quantum correlation of photon pairs. The two-photon interference was observed with a visibility of 84% when the two arm lengths were balanced.
Feasible Entanglement Purification for Quantum Communication (2000)

The distribution of entangled states between distant locations will be essential for the future large scale realization of quantum communication schemes such as quantum cryptography and quantum teleportation. Because of the unavoidable noise in the quantum communication channel, the entanglement between two particles is more and more degraded the further they propagate. Entanglement purification is thus essential to distill highly entangled states from less entangled ones. Existing general purification protocols are based on the quantum controlled-NOT (CNOT) or similar quantum logic operations, which are very difficult to implement experimentally. Present realizations of CNOT gates are much too imperfect to be useful for long-distance quantum communication. Here we present a feasible scheme for the entanglement purification of general mixed entangled states, which does not require any CNOT operations, but only simple linear optical elements. Since the perfection of such elements is very high, the local operations necessary for purification can be performed with the required precision. Our procedure is within the reach of current technology and should significantly simplify the implementation of long-distance quantum communication.
Long range surface plasmon resonance (LRSPR) based highly sensitive refractive index sensor using Kretschmann prism coupling arrangement (2016)

Long range surface plasmon resonance (LRSPR) when exploited for sensing purpose exhibit less losses in comparison to the sensors based on conventional SPR technique leading to the development of highly sensitive refractive index sensor. In order to excite long range surface plasmon (LRSP) mode, a high refractive index prism is used as coupler and a thin metal layer is sandwiched between a dielectric having similar refractive index with that of another semi-infinite dielectric. LRSP mode has been excited in symmetric configuration where metal (Au) layer is sandwiched between the two similar refractive index dielectrics (LiF thin film and a fixed concentration of sugar solution) for realization of a refractive index sensor. When the concentration of sugar solution is slightly increased from 30% to 40%, the LRSPR angle increases from 64.6° to 67.9° and the sensor is found to be highly sensitive with sensitivity of 0.0911 °/(mg/dl).
New techniques for extracting features from protein sequences (2001)

In this paper we propose new techniques to extract features from protein sequences. We then use the features as inputs for a Bayesian neural network (BNN) and apply the BNN to classifying protein sequences obtained from the PIR (Protein Information Resource) database maintained at the National Biomedical Research Foundation. To evaluate the performance of the proposed approach, we compare it with other protein classifiers built based on sequence alignment and machine learning methods. Experimental results show the high precision of the proposed classifier and the complementarity of the bioinformatics tools studied in the paper.
Fused Double Donor Design with a Cross-Conjugated Dibenzosilin for Dye-Sensitized Solar Cells (2023)

Dye-sensitized solar cells (DSCs) can provide a clean energy solution to growing energy demands. In order to have devices of high performance, sensitizers that are able to absorb in the near-infrared region (NIR) are needed. Stronger electron donors are needed for intramolecular charge-transfer sensitizers to access longer wavelength photons. Thus, two novel organic dyes with a cross-conjugated dibenzosilin double donor design are studied herein. The double donor delocalizes multiple filled orbitals across both amine donors due to the fused design that planarizes the donor as observed computationally, which improves intramolecular charge-transfer strength. The dyes are studied via density functional theory (DFT), optical spectroscopy, electrochemistry, and in DSC devices. The studies indicate that the dye design can reduce recombination losses, allowing for improved DSC device performances relative to a single arylamine donor. The reduction in recombination losses is attributed to the six alkyl chains that are incorporated into the donor, which offer good surface protection.
Evaluation of the Conservation Culture Development in Shandong Province, China (2012)

As conservation culture turns to be a public issue in China, an increasing number of scholars and agencies are dedicating to studying and building the conservation culture index to evaluate regional conservation culture development. Shandong, a province with large population, booming economy, and scarce land and water resources, should well recognize its status quo and trend of conservation culture construction for a sustainable future. According to local natural conditions and socio-economic development status of the 17 cities in Shandong, the authors firstly select 18 indicators from a wide range covering natural resources, social and economic development, and environment conditions, and build a conservation culture index system. Next, we standardize the values of all indicators and calculate the sub-indices of conservation culture in three dimensions, economic and social structure, resources and environmental function, and coordination degree between human and nature. Then, we weight the three sub-indices, comprise the conservation culture index of each of the 17 cities, and assess their conservation culture development levels. Finally, based on the assessment and grading of conservation culture development levels of the 17 cities, the authors put forwards some corresponding countermeasures to integrate social, economic and ecological development, and further upgrade the conservation culture development of the province.
PSVIII-18 Protective effect of Lactobacillus Casei Zhang on E. coli induced mastitis in mice (2020)

Abstract Mastitis is an acute, obvious and harmful clinical disease in mammals. It is also one of the productive diseases with high incidence, rapid epidemic and great economic loss in dairy farming. Antibiotics are the first choice for the treatment of infectious mastitis, but the long-term use of antibiotics in large quantities will lead to the emergence of antibiotic residues and bacterial resistance, which is harmful to the health of both human and animals. As a potential substitute of antibiotics, Lactobacillus has great potential in the control of pathogenic microorganisms. The purpose of this study was to explore the effect of Lactobacillus casei Zhang (L. Casei Zhang) on the prevention of E. coli-induced mastitis in mice and its protective effect on the damage of the blood and milk barrier. Intramammary administration of E. coli was used to establish a mouse mastitis model. Control group (PBS), E. coli administration group, and L. casei Zhang pretreatment plus E. coli administration group were set up respectively and the mammary gland samples were collected for analysis. The results showed that: L. casei Zhang could significantly reduce the degree of breast tissue damage and the content of inflammatory factors TNF-α，IL-6 and IL-1β (P &amp;lt; 0.05). In addition, the expression of tight junction proteins ZO-1, Claudin-3 and Occludin in the mammary gland tissues of mice was significantly promoted (P &amp;lt; 0.05). In conclusion, intramammary administration of L. casei Zhang could effectively reduce the inflammation of the mouse mammary gland induced by E. coli, and this protection is achieved by promoting the expression of the blood-milk barrier tight junction proteins.
A Panel of Three Markers Hyper- and Hypomethylated in Urine Sediments Accurately Predicts Bladder Cancer Recurrence (2014)

Given their superior sensitivity and specificity in urine sediments, a combination of hyper- and hypomethylated markers may help avoid unnecessary invasive exams and reveal the importance of DNA methylation in bladder tumorigenesis.
Map integration of human trajectory with sitting/standing position using LRF and Kinect sensor (2012)

This paper presents a service oriented map that includes a) environment shape, b) human walking trajectory, and c) human sitting/standing position. Such information is important for a robot that provides services to human beings. Environmental shape (a) and human walking trajectory (b) are obtained by LRF. Human sitting/standing position (c) is obtained from Microsoft Kinect sensor by actively positioning and orienting the sensor to confirm human posture. A combined algorithm to obtain an integrated map is described, and experimental results follow.
Characterization of Penile Erectile States Using External Computer-Based Monitoring (1987)

The states of penile erection have not been quantified to establish their relationship to intracorporal fluid pressure and to soft tissue constraint. Computer-based circumferential rigidity sensing during erectile cycles now permits circumferential size and rigidity characterization. Measurements during dynamic infusion cavernometry and cavernosography relate intracorporal pressure and axial rigidity to circumference and circumferential rigidity characterization. Tumescence/rigidity coupling and tissue elastic contributions are identified from the combined data.
Microbial factors in disease emergence illustrated by streptococcal toxic shock syndrome (1997)

Factors contributing to the emergence of infectious diseases will be reviewed briefly to provide a background for a discussion of the sharp decline in the occurrence of group A streptococcal disease that began early in this century before the use of antibiotics, and the emergence of streptococcal toxic shock syndrome (STSS) in the last decade. The strains of group A streptococci that cause STSS have been dubbed ‘the flesh-eating bacteria’ by the media, and are the focus of this paper. Be aware that none of the factors contributing to disease emergence operates in isolation; there is endless overlap and interplay.

‘Microbial traffic’ introduces microbes to new domains where they find people and animals unprotected by prior experience. They hitchhike along with all of us in travel and commerce, accompanying the one million air passengers that fly each day. How many alien microbes did they bring with them right into the conference hall when they arrived in Kyoto with participants of this symposium?

But people are not the only expediters of international movement of microbes. Pathogens can be flown in on fresh foods rushed to our dinner tables. Influenza viruses migrate with aquatic birds that carry viral genes to new venues to combine through genetic reassortment with resident flu viruses. As in the past, new flu viruses can emerge from this union that possess unusual virulence to spread around the world. Thus, microbial traffic facilitates the emergence of infectious diseases from microbes that already exist and microbes that emerge from genetic changes and evolutionary selection [1–3].

Disease vectors travel also to new environments. Ocean transport ships provide passage for rodent stowaways and insects that breed in recycled vehicle tyres, carrying them to new domains where they find new ecological niches. Insect vectors especially are on the loose again, …
ChemInform Abstract: Zeolites as Catalysts (2002)

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.
Intentionality, an essay in the philosophy of mind (1983)

John Searle's Speech Acts (1969) and Expression and Meaning (1979) developed a highly original and influential approach to the study of language. But behind both works lay the assumption that the philosophy of language is in the end a branch of the philosophy of the mind: speech acts are forms of human action and represent just one example of the mind's capacity to relate the human organism to the world. The present book is concerned with these biologically fundamental capacities, and, though third in the sequence, in effect it provides the philosophical foundations for the other two. Intentionality is taken to be the crucial mental phenomenon, and its analysis involves wide-ranging discussions of perception, action, causation, meaning, and reference. In all these areas John Searle has original and stimulating views. He ends with a resolution of the 'mind-body' problem
Virtual Spring–Damping System for Flow-Induced Motion Experiments (2015)

Flow-induced motion (FIM) experiments of a single circular cylinder or multiple cylinders in an array involve several configuration and hydrodynamic parameters, such as diameter, mass, damping, stiffness, spacing, Reynolds number, and flow regime, and deviation from circular cross section. Due to the importance of the FIM both in suppression for structural robustness and in enhancement for hydrokinetic energy conversion, systematic experiments are being conducted since the early 1960s and several more decades of experimentation are required. Change of springs and dampers is time consuming and requires frequent recalibration. Emulating springs and dampers with a controller makes parameter change efficient and accurate. There are two approaches to this problem: The first involves the hydrodynamic force in the closed-loop and is easier to implement. The second called virtual damping and spring (Vck) does not involve the hydrodynamic force in the closed-loop but requires an elaborate system identification (SI) process. Vck was developed in the Marine Renewable Energy Laboratory (MRELab) of the University of Michigan for the first time in 2009 and resulted in extensive data generation. In this paper, the second generation of Vck is developed and validated by comparison of the FIM experiments between a Vck emulated oscillator and an oscillator with physical springs and dampers. The main findings are: (a) the Vck system developed keeps the hydrodynamic force out of the control-loop and, thus, does not bias the FIM, (b) The controller-induced lag is minimal and significantly reduced compared to the first generation of Vck built in the MRELab due to use of an Arduino embedded board to control a servomotor instead of Labview, (c) The SI process revealed a static, third-order, nonlinear viscous model but no need for dynamic terms with memory, and (d) The agreement between real and virtual springs and dampers is excellent in FIM including vortex-induced vibrations (VIVs) and galloping measurements over the entire range of spring constants and velocities tested (16,000 &lt; Re &lt; 140,000).
Study of tobacco plant as a possible nutritive protein source (2010)

The changes in the activity of enzyme polyphenol oxidase, the concentration of total soluble phenolic compounds and soluble protein content in different tobacco cultivars (Virginia and Burley) during cultivation, then in a combined curing model system were studied. The latter was a special combination of air-curing and flue-curing methods followed by a long fermentation period to optimize the treatment of tobacco plants used both as protein sources and starting materials in tobacco industry. The results suggest that a cultivation period of 13–14 weeks could be better for tobacco plants as protein sources, however, for starting materials for industrial use 16–17 weeks are optimal. It was found a four-week curing period could be the best for two tobacco cultivars (Virginia and Burley) in the case of using them both as protein sources and starting materials in tobacco industry.
Vascular smooth muscle cell apoptosis is a critical event in vessel remodeling during human pregnancy (2006)

Remodeling of resistance arteries typically involves medial thickening through smooth muscle cells (SMC) hyperplasia and extra‐cellular matrix deposition. The result is reduced lumen diameter and increased resistance. When uterine spiral arteries remodel in human pregnancy the opposite occurs. Loss of endothelium and SMC results in medial ablation, luminal expansion and decreased resistance. This change facilitates greater blood flow to the fetus however the underlying mechanisms are poorly defined. Shallow or incomplete fetal trophoblast invasion and limited remodeling are associated with pregnancy complications like pre‐eclampsia. We tested the hypothesis that vascular SMC apoptosis is a key step in spiral artery remodeling during pregnancy and focused on interactions between trophoblast and SMC. Co‐culture of human aortic SMC (HASMC) with primary first trimester human cytotrophoblasts (CTB) or a trophoblast cell line, SGHPL‐4, caused HASMC apoptosis and could be blocked by caspase inhibition with zVAD‐fmk. CTB in culture produced the apoptotic cytokines Fas ligand and TRAIL and receptors for these cytokines were detected in term spiral artery sections. A Fas‐activating antibody or rhTRAIL induced HASMC apoptosis; blocking Fas or TRAIL receptor activation significantly inhibited CTB‐induced HASMC apoptosis in co‐culture. We propose that trophoblast‐derived apoptotic cytokines cause SMC apoptosis in uterine spiral arteries thus contributing to vessel remodeling during pregnancy. Supported by a Wellcome Trust UK grant (069939).
Backtracking Algorithmic Complexity Attacks against a NIDS (2006)

Network Intrusion Detection Systems (NIDS) have become crucial to securing modern networks. To be effective, a NIDS must be able to counter evasion attempts and operate at or near wire-speed. Failure to do so allows malicious packets to slip through a NIDS undetected. In this paper, we explore NIDS evasion through algorithmic complexity attacks. We present a highly effective attack against the Snort NIDS, and we provide a practical algorithmic solution that successfully thwarts the attack. This attack exploits the behavior of rule matching, yielding inspection times that are up to 1.5 million times slower than that of benign packets. Our analysis shows that this attack is applicable to many rules in Snorts ruleset, rendering vulnerable the thousands of networks protected by it. Our countermeasure confines the inspection time to within one order of magnitude of benign packets. Experimental results using a live system show that an attacker needs only 4.0 kbps of bandwidth to perpetually disable an unmodified NIDS, whereas all intrusions are detected when our countermeasure is used.
Steering driftless nonholonomic systems by control quanta (2002)

We consider the problem of steering a class of nonholonomic systems, namely systems that are feedback equivalent to a strictly triangular form, which is considerably larger than other classes for which the steering problem, has been given closed form solutions in the literature. The proposed solution consists in the application of a finite concatenation of finite-support control actions chosen among a finite set, suitable selected in the input space, each resulting in a quantum change in the system state. The method results in a closed form algorithm which is exact up to an arbitrary tolerance.