gebhart/patrepeval huggingface dataset:
Rapid Screening of HIV Reverse Transcriptase and Integrase Inhibitors (2014)

Although a number of anti HIV drugs have been approved, there are still problems with toxicity and drug resistance. This demonstrates a need to identify new compounds that can inhibit infection by the common drug resistant HIV-1 strains with minimal toxicity. Here we describe an efficient assay that can be used to rapidly determine the cellular cytotoxicity and efficacy of a compound against WT and mutant viral strains. The desired target cell line is seeded in a 96-well plate and, after a 24 hr incubation, serially dilutions of the compounds to be tested are added. No further manipulations are necessary for cellular cytotoxicity assays; for anti HIV assays a predetermined amount of either a WT or drug resistant HIV-1 vector that expresses luciferase is added to the cells. Cytotoxicity is measured by using an ATP dependent luminescence assay and the impact of the compounds on infectivity is measured by determining the amount of luciferase in the presence or the absence of the putative inhibitors. This screening assay takes 4 days to complete and multiple compounds can be screened in parallel. Compounds are screened in triplicate and the data are normalized to the infectivity/ATP levels in absence of target compounds. This technique provides a quick and accurate measurement of the efficacy and toxicity of potential anti HIV compounds.
Piezoelectric energy harvesting using diaphragm structure (2003)

Energy harvesting using piezoelectric material is not a new concept, but its generation capability has not been attractive for mass energy generation. For this reason, little research has been done on the topic. Recently, wearable computer concepts, as well as small portable electrical devices, are a few motivations that have ignited the study of piezoelectric energy harvesting again. The theory behind cantilever type piezoelectric elements is well known, but the transverse moving diaphragm elements, which can be used in pressure type energy generation is not yet fully developed. The power generation in a diaphragm depends on several factors. Among them, the thickness of each layer is important. In this paper, two diaphragm structures, unimorph and bi-morph, were used to calculate energy generation with varying thickness ratio using piezoelectric constitutive equation. The results of this analysis are presented with an eye toward guidelines for design of useful energy harvesting structure.
Autologous transfusion techniques: a systematic review of their efficacy (2004)

Shortages of donor blood and fears of transmitted infections have prompted the use of a range of blood-sparing techniques in the peri-operative period. We conducted a systematic review of three techniques that involve the re-infusion of a patient's blood--pre-operative autologous blood deposit (PAD), acute normovolaemic haemodilution (ANH), and cell salvage (CS). We examined the effects of these interventions on the need for peri-operative allogeneic red blood cell transfusion and on clinical outcomes. Controlled clinical studies were identified by computer searches of comprehensive electronic databases and bibliographic searches of published articles. The literature search retrieved a total of 68 randomized trials (RCTs) and 81 controlled observational studies that included data from over 34 000 individuals. In summary, the RCTs found that autologous transfusion techniques consistently reduced the frequency of allogeneic transfusions, with intervention effect sizes ranging from a relative 63% reduction (95% CI 46-74%) with PAD, to 42% (27-53%) with CS and to 31% (16-44%) with ANH. Non-randomized studies reported larger effect sizes than RCTs. PAD increased overall transfusion rates by 30% (95% CI 12-48%) and reduced pre-operative haemoglobin levels by an average of 1.23 g dL(-1). Intervention effects were substantially reduced when these techniques were performed under transfusion protocols. Interpretation of the studies was hampered by serious methodological weaknesses, particularly inadequate randomization techniques, unblinded measurements and the subjective nature of the outcome variables. The studies reported few clinical outcome and adverse event data. Previous claims regarding reduced rates of mortality and infection with autologous transfusions were not confirmed.
A Robust Switched-Capacitor CDC (2018)

A capacitance-to-digital converter (CDC) designed to possess negligible sensitivity to non-ideal circuit parameters is presented in this paper. The scheme is based on switched capacitor integrating technique and the conversion process is such that the final output is fundamentally insensitive to leakage resistance and stray capacitance of the sensor, offset voltage and bias current of the opamp, delay, offset voltage, and bias current of the comparator, leakage current, delay, and charge injection of the switches employed, and so on. Such a characteristic is highly useful for precision measurement. The proposed CDC achieves it without any special compensating circuits, unlike some of the existing CDCs that partially meet the above feature. The performance of the CDC has been experimentally evaluated. Results show high insensitivity to the non-ideal circuit parameters. In addition, the worst case non-linearity error of the prototype CDC was found to be less than 0.1%, when tested for a range of 10 to 400 pF.
Gallium-68 Complex of a Macrobicyclic Cage Amine Chelator Tethered to Two Integrin-Targeting Peptides for Diagnostic Tumor Imaging (2011)

Tumor-targeting peptides radiolabeled with positron-emitting (68)Ga are promising candidates as new noninvasive diagnostic agents for positron emission tomography (PET). The targeting peptides are tethered to a chelator that forms a stable coordination complex with Ga(3+) that is inert to dissociation of Ga(3+)in vivo. Metal complexes of macrobicyclic hexaamine "sarcophagine" (sar = 3,6,10,13,16,19-hexaazabicyclo[6.6.6]icosane) ligands exhibit remarkable stability as a result of the encapsulating nature of the cage amine ligand. A Ga(3+) sarcophagine complex, [Ga-(1-NH(3)-8-NH(2)-sar)](4+), has been characterized using X-ray crystallography, demonstrating that Ga(3+) is coordinated to six nitrogen atoms in a distorted octahedral complex. A bifunctional derivative of (NH(2))(2)sar, possessing two aliphatic linkers with carboxylic acid functional groups has been attached to two cyclic-RGD peptides that target the α(v)β(3) integrin receptor that is overexpressed in some types of tumor tissue. This dimeric species can be radiolabeled with (68)Ga(3+) in >98% radiochemical yield and (68)Ga(3+) does not dissociate from the ligand in the presence of transferrin, an endogenous protein with high affinity for Ga(3+). Biodistribution and micro-PET imaging studies in tumor-bearing mice indicate that the tracer accumulates specifically in tumors with high integrin expression. The high tumor uptake is coupled with low nonspecific uptake and clearance predominantly through the kidneys resulting in high-quality PET images in animal models.
Sizing Internet Router Buffers, Active Queue Management, and the Lur'e Problem (2006)

In this paper we consider the design of control strategies for implementation in a recently proposed active queue management (AQM) scheme, active drop-tail (ADT) (Stanojevic et al., 2006), The basic idea underlying ADT is to adjust the queue length of a drop-tail buffer to regulate the utilization of a link carrying Internet traffic in order to reduce queuing delays in the network. A basic problem in the design of ADT is to design appropriate strategies to regulate the target utilization using the buffer queue as a control input. This problem is challenging due to the stochastic and time-varying nature of communication networks. Our contribution in this paper is to relate the design of control strategies for this AQM to the classical Lur'e problem. Our formulation naturally accounts for the time-variations and randomness inherent in communication networks, and enables us to design AQMs with guaranteed convergence (under mild and realistic assumptions). Packet level simulations are given to demonstrate the efficacy of our design methodology
Alkylsubstituted Thienothiophene Semiconducting Materials: Structure−Property Relationships (2009)

A family of conjugated polymers with fused structures consisting of three to five thiophene rings and with the same alkyl side chains has been synthesized as a means to understand structure-property relationships. All three polymers showed well-extended conjugation through the polymer backbone. Ionization potentials (IP) ranged from 5.15 to 5.21 eV; these large values are indicative of their excellent oxidative stability. X-ray diffraction and AFM studies suggest that the polymer with the even number of fused thiophene rings forms a tight crystalline structure due to its tilted side chain arrangement. On the other hand, the polymers with the odd number of fused thiophene rings packed more loosely. Characterization in a field-effect transistor configuration showed that the mobility of the polymer with the even number of rings is 1 order of magnitude higher than its odd-numbered counterparts. Through this structure-property study, we demonstrate that proper design of the molecules and properly arranged side chain positions on the polymer backbone can greatly enhance polymer electronic properties.
A method for identifying faulty cells using a classification tree-based UE diagnosis in LTE (2017)

The latest advances in wireless technologies have led to a proliferation of data mobile devices and services. As a consequence, mobile networks have experienced a significant increase in data traffic, while voice traffic has shown nearly no growth. It is therefore essential for operators to understand the data traffic behavior at the user level in order to ensure a good customer experience. In the radio access networks (RANs), traditional solutions based on cell-level measurements are not adequate to analyze performance of individual users. Instead, novel alternatives such as the use of call traces and the definition of new user-centric indicators will provide detailed and valuable information for each connection. One of the key measurements related to data services is the user throughput. In this work, the user throughput is adopted as the main attribute to conduct diagnosis in the RAN, which has typically been the bottleneck for data services. To that end, a binary classification tree is proposed to determine the root cause of poor throughput in user-level data sessions. Then, this information is aggregated at the cell level in order to provide effective diagnosis of degraded cells. In particular, a correlation-based analysis of the cell status is proposed in order to identify abnormal cell behaviors in an automatic way. Evaluation has been carried out with datasets from live cellular networks. Results show that the proposed diagnosis approach is an effective means to identify the main factors that limit the user throughput in network cells.
In-line optical fiber sensors based on cladded multimode tapered fibers (2004)

The use of uniform-waist cladded multimode tapered optical fibers is demonstrated for evanescent wave spectroscopy and sensors. The tapering is a simple, low-loss process and consists of stretching the fiber while it is being heated with an oscillating flame torch. As examples, a refractive-index sensor and a hydrogen sensor are demonstrated by use of a conventional graded-index multimode optical fiber. Also, absorbance spectra are measured while the tapers are immersed in an absorbing liquid. It is found experimentally that the uniform waist is the part of the taper that contributes most to the sensor sensitivity. The taper waist diameter may also be used to adjust the sensor dynamic range.
In Vivo Imaging of Molecularly Targeted Phage (2006)

Rapid identification of in vivo affinity ligands would have far-reaching applications for imaging specific molecular targets, in vivo systems imaging, and medical use. We have developed a high-throughput method for identifying and optimizing ligands to map and image biologic targets of interest in vivo. We directly labeled viable phage clones with far-red fluorochromes and comparatively imaged them in vivo by multichannel fluorescence ratio imaging. Using Secreted Protein Acidic and Rich in Cysteine (osteonectin) and vascular cell adhesion molecule-1 as model targets, we show that: 1) fluorescently labeled phage retains target specificity on labeling; 2) in vivo distribution can be quantitated (detection thresholds of approximately 300 phage/mm(3) tissue) throughout the entire depth of the tumor using fluorescent tomographic imaging; and 3) fluorescently labeled phage itself can serve as a replenishable molecular imaging agent. The described method should find widespread application in the rapid in vivo discovery and validation of affinity ligands and, importantly, in the use of fluorochrome-labeled phage clones as in vivo imaging agents.
High refractive-index microspheres of optical cavity structure (2003)

Microspheres of refractive index of nD&gt;2 have been investigated. The organic-inorganic hybrid microspheres of refractive index nD=1.70–1.72 were prepared at room temperature by the vibrating orifice technique using titanium alkoxide and silane coupling reagents as starting materials. Subsequently heating the microspheres at 400–450 °C resulted in increasing their refractive indices to nD=2.10–2.25 with keeping good spherical shape. Rhodamine 6G-doped microspheres of nD=1.72 were also prepared at room temperature and the lasing from them was performed by pumping by second-harmonic pulses of Q-switched Nd–yttritium–aluminum–garnet laser.
Preparation of collagen scaffolds with controlled pore structures and improved mechanical property for cartilage tissue engineering (2013)

Appropriate pore structures and mechanical properties are required for scaffolds that are used for tissue engineering and regenerative medicine. In this study, pre-prepared ice particulates were used as a porogen material to prepare collagen porous scaffolds with well-controlled pore structures and improved mechanical properties. Porogen ice particulates initiated the formation of interconnected large spherical pores surrounded by small pores. The large spherical pores were well compacted and increased the elastic modulus of the scaffolds. The unique pore structures facilitated cell penetration, resulting in a homogeneous cell distribution throughout the scaffolds. The excellent mechanical properties protected the scaffolds from deformation during cell culturing and implantation. The collagen porous scaffolds facilitated cartilage regeneration when bovine articular chondrocytes were cultured in these scaffolds. The use of pre-prepared ice particulates as a porogen material proved to be a useful method to control the pore structure and improve the mechanical properties of collagen-based porous scaffolds.
Perspectives on Anti-HER Monoclonal Antibodies (2002)

The ability of Herceptin to prolong survival in women with HER2-overexpressing breast tumors has proven the concept of using humanized or chimeric monoclonal antibodies (MAbs) for cancer therapy. MAbs have been developed that are specific for many tumorigenic molecules and receptors. They can potentially be used to treat a range of solid tumors. Among the most promising targets for therapy are members of the human epidermal growth factor receptor (HER/ErbB) family, particularly HER1 and HER2. Several MAbs have been produced that are directed against HER1. One of these agents, cetuximab (Erbitux), is now advanced in clinical development. HER2 is also a key target and methods are being investigated to maximize the effect of using MAbs to inhibit this receptor. One approach aims to augment the efficacy of trastuzumab (Herceptin) by coupling it to a chemotherapeutic agent, thus enabling the delivery of cytotoxic therapy at a cellular level. Another opportunity is based on research that shows that HER2 acts as a dimerization partner for other HER receptors and consequently is important in HER-ligand-dependent tumor growth. Therefore, anti-HER2 MAbs that inhibit the association of HER2 with other HER family members have the potential to be highly effective. This article reviews some of these alternative approaches to MAb-based anti-HER therapy that will hopefully improve treatment outcome for patients with a range of solid tumors.
Promiscuous ligands and attractive cavities: how do the inhaled anesthetics work? (2001)

The inhaled anesthetics were officially introduced to American medicine more than 160 years ago and rank among the most important medical advances in our time. These drugs are used to render patients insensible over twenty million times each year and are the most dangerous of all drugs that physicians currently use. An entire medical specialty, anesthesiology, has arisen out of the need for the special training to administer them safely. Nevertheless, side effects, toxicity, and long-term cognitive problems continue to plague their use, especially in the very sick or aged. Hence, it is essential that we develop an understanding of their molecular pharmacology so that safer alternatives can be developed.
UV-induced apoptosis in skin equivalents: inhibition by phorbol ester and Bcl-2 overexpression. (1995)

To determine the role of apoptosis in epidermal homeostasis and to identify its regulators in skin, we have developed and characterised a physiologically relevant in vitro model of epidermal apoptosis. First, we show that keratinocyte cell death can be induced by ultraviolet irradiation within the stratified epidermis of the skin equivalent in an in vivo-like manner. DNA fragmentation and changes in the patterns of expression of p53 and Bcl-2 suggest that the mechanisms operating in UV-induced apoptosis in the skin equivalent are controlled by these factors. Secondly, we demonstrate that apoptosis in this model is amenable to modulation by exogenous factors present in the culture medium, such as phorbol ester, and by tranfected genes, as shown by overexpression of bcl-2. These studies show that the skin equivalent is a valuable model in which to determine the controllable steps of the apoptotic pathway independently of the immune system and to correlate apoptosis to the physiologic state of the keratinocyte.
One For All: A Mutual Enhancement Method for Object Detection and Semantic Segmentation (2019)

Generally, most approaches using methods such as cropping, rotating, and flipping achieve more data to train models for improving the accuracy of detection and segmentation. However, due to the difficulties of labeling such data especially semantic segmentation data, those traditional data augmentation methodologies cannot help a lot when the training set is really limited. In this paper, a model named OFA-Net (One For All Network) is proposed to combine object detection and semantic segmentation tasks. Meanwhile, using a strategy called “1-N Alternation” to train the OFA-Net model, which can make a fusion of features from detection and segmentation data. The results show that object detection data can be recruited to better the segmentation accuracy performance, and furthermore, segmentation data assist a lot to enhance the confidence of predictions for object detection. Finally, the OFA-Net model is trained without traditional data augmentation methodologies and tested on the KITTI test server. The model works well on the KITTI Road Segmentation challenge and can do a good job on the object detection task.
Side-chain interactions between sulfur-containing amino acids and phenyalanine in .alpha.-helixes (1995)

The side-chain-side-chain interaction between Phe residues and sulfur-containing residues (Cis and Met) in the two possible orientations at positions i, i + 4 of alpha-helices is described. We have analyzed the contribution to helical stability of the above interactions by studying eight polyalanine-based peptides differing at the residues at positions 9 and 13. These two positions were independently mutated from Ala (AA), to Cys (AC and CA), Met (AM and MA), and Phe (AF and FA) and to the pairs Phe-Met (FM), Met-Phe (MF), Phe-Cys (FC), and Cys-Phe (CF). The intrinsic helical propensities of Cys, Met, and Phe were found to be those previously described in the algorithm AGADIR. NMR analysis of the FM, MF, FC, and CF peptides showed the formation in aqueous solution of contacts between the aromatic ring and the side chains of Cys or Met, at the two i, i + 4 orientations. CD studies demonstrated the important contribution of two of these interactions (FM and FC) to alpha-helix stability (up to 2 kcal mol-1 in the Phe-Cys pair). Statistical analysis of the protein database provides a rationale for the stereospecificity and free energies of the interactions. The very favorable interaction between an aromatic ring and a sulfur-containing amino acid explains why in the protein database around 50% of the sulfur atoms are contacting aromatic rings (Reid et al., 1985).
Intelligent Supervision and Integrated Fault Detection and Diagnosis for Subsea Control Systems (2007)

This paper proposes an artificial intelligence based framework for integrated fault detection and diagnosis to support supervision and decision making applicable to subsea control systems. Instrumentation, electrical, electronic, hydraulic and communication subsystems are considered. This approach may contribute to minimizing well shut-down and production losses due to unexpected faults on any subsea control system component or subsystem. It may also contribute to achieving incipient fault detection and appropriate fault identification to support and improve troubleshooting, decision making and maintenance tasks (preventive maintenance).
Establishment of an embryonic stem (ES) cell line derived from a non‐obese diabetic (NOD) mouse: in vivo differentiation into lymphocytes and potential for germ line transmission (1999)

A non-obese diabetic (NOD) mouse-derived embryonic stem (ES) cell line has been stably maintained in an undifferentiated state with a characteristic ES cell-like morphology, expressing the stem cell marker alkaline phosphatase, and displaying a normal diploid karyotype. After injecting the NOD-ES cells into blastocysts, chimeric mice were obtained. Small but significant numbers of lymphocytes expressed the NOD-derived MHC allele. When a chimeric mouse was mated with C57BL/6 mice, an agouti mouse was obtained, having the NOD-derived H-2 I-A(beta)g7 haplotype. Thus, an NOD-ES cell line which can differentiate into lymphocytes with potential for germ line transmission was successfully established.
Intrinsic sites of transcription termination and pausing in the c-myc gene. (1988)

We have studied transcription elongation and termination in the human c-myc gene. Transcription of c-myc gene sequences with purified mammalian RNA polymerase II revealed several sites of transcription termination and pausing in the vicinity of the exon 1-intron 1 junction. This region previously has been shown to block transcription elongation in vivo by nuclear run-on analysis (D. Bentley and M. Groudine, Nature [London] 321:702-706, 1986). These sites were recognized by purified RNA polymerase II, and we therefore designated them intrinsic sites of termination and pausing. Two of these sites cause termination of RNA polymerase III transcription as well. RNA polymerase II terminated transcription in a cluster of seven consecutive T residues in the nontranscribed strand and paused during transcription at three additional sites in this region. The intrinsic sites of transcription termination and pausing described here correspond closely to the 3' ends of transcripts synthesized in Xenopus oocytes injected with plasmids containing the c-myc termination region (D. Bentley and M. Groudine, Cell 53:245-256, 1988). This correspondence suggests that the intrinsic recognition of these termination and pause sites by purified RNA polymerase II may play a role in the transcription elongation block observed in vivo.