gebhart/patrepeval huggingface dataset:
The Fluorescent Protein Color Palette (2007)

Advances in fluorescent protein development over the past 10 years have led to fine-tuning of the Aequorea victoria jellyfish color palette in the emission color range from blue to yellow, while a significant amount of progress has been achieved with reef coral species in the generation of monomeric fluorescent proteins emitting in the orange to far-red spectral regions. It is not inconceivable that near-infrared fluorescent proteins loom on the horizon. Expansion of the fluorescent protein family to include optical highlighters and FRET biosensors further arms this ubiquitous class of fluorophores with biological probes capable of photoactivation, photoconversion, and detection of molecular interactions beyond the resolution limits of optical microscopy. The success of these endeavors certainly suggests that almost any biological parameter can be investigated using the appropriate fluorescent protein-based application.
In vitro and in vivo growth inhibition and G1 arrest in human cancer cell lines by diaminophenyladamantane derivatives (2004)

We describe the discovery of a novel series of anticancer adamantane derivatives which induce G1 arrest in Colo 205 and HT 29 colon cancer cells. Seven adamantane derivatives were screened for their activity in vitro against 60 human cancer cell lines in the National Cancer Institute (NCI)'s Anticancer Drug Screen system. The relationships between structure and in vitro anticancer activity are discussed. 1,3-Bis(4-(4-amino-3-hydroxyphenoxy)phenyl)adamantane (1,3-DPA/OH/NH2) and 2,2-bis(4-(4-amino-3-hydroxyphenoxy)phenyl)adamantane (DPA) exhibited strong growth inhibitory on anticancer activities in vitro. The IC50s of 1,3-DPA/OH/NH2 (NSC-706835) and DPA (NSC-706832) were found to be < 3 microM against 45 (85%) and 48 (91%) cell lines, respectively. 2,2-Substituted adamantane derivatives exhibited stronger growth inhibition on anticancer activities in vitro than the corresponding 1,3-substituted analogs. Very strong growth inhibition of 2,2-bis(4-aminophenyl)adamantane (NSC-711117) was observed against two colon cancer lines (HT-29 and KM-12), one CNS cancer line (SF-295) and one breast cancer line (NCI/ADR-RES) with IC50 < 1.0 microM, i.e. 0.1, 0.01, 0.059 and 0.079 microM, respectively. In addition, we also examined the in vitro and in vivo effects of DPA on three human colon cancer cells. DPA-treated Colo 205 and HT-29 cells were arrested at G0/G1 as analyzed by flow cytometric analysis. The DPA-induced cell growth inhibition was irreversible after removal of DPA. The in vivo effect of tumor growth suppression by DPA was also observed on colon Colo 205 xenografts. No acute toxicity was observed after an i.p. challenge of DPA in ICR nude mice weekly. These results suggest that DPA appears to be a new potentially less toxic modality of cancer therapy.
Adjuvant arthritis and immunity to the mycobacterial 65 kDa heat shock protein (1992)

The mycobacterial 65 kDa heat shock protein (HSP65) is of critical significance in the model of adjuvant arthritis (AA). Arthritogenic and protective T cell clones obtained from arthritic rats recognized the 180-188 sequence of HSP65. Previous reports have shown that administration of HSP65 prior to disease induction led to resistance to arthritis in the AA model and in several other models of experimental arthritis. Here, we report the development of immunity to HSP65 and the critical 180-188 epitope during the course of AA. Following Mycobacterium tuberculosis (MT) immunization both antibodies and T cell responses to HSP65 were detected. Proliferative responses to the 180-188 epitope were seen exclusively in the local draining lymph node cells at day 14 after immunization. The anatomical distribution and course of T cell responses to HSP65 and its 180-188 epitope are compatible with T cell regulated control of the disease. Although lower HSP65 antibody levels were observed in the animals with severe arthritis, in individual animals no evidence was obtained for a relationship between development of HSP65 humoral immunity and arthritis severity. Nevertheless, during disease exacerbation, elicited by HSP65 immunization during disease development, elevated T cell responses against HSP65 and its 180-188 epitope were found. In contrast, we obtained evidence that successful transfer of arthritis resistance to naive recipients depends on the transfer of HSP65 specific T cells. On the basis of these results, it seems that HSP65 plays a crucial role in the T cell regulatory events involved in both the induction of, and protection against, AA.(ABSTRACT TRUNCATED AT 250 WORDS)
A strategy for C-based verification (2002)

This paper describes a simple set of tools and techniques that can be used to develop test and verification software in the C environment and interface these tests to a Verilog/VHDL simulation. Particular attention is given to a 'virtual processor' interface between the C-based test code and the simulation engine.
Substance P &ndash; Structure-Activity Studies and the Development of Antagonists (1984)

Various attempts to developing antagonists for substance P (SP) and related peptides, based on our past experience with angiotensin, kinins, and neurotensin, were unsuccessful. The particular features of SP, namely the high activity of C-terminal partial sequences in some pharmacological tests were used to develop one hexa and several octapeptide antagonists. Weak antagonists were obtained with a single modification, namely the replacement of Leu10 with trp in the sequences SP (6–11), SP (4–11) and SP (1–11). The affinity of octa and undecapeptide antagonists could be increased by using two (in positions 7 and 9 or 7 and 10) or 3 (in position 7, 9 and 10) substitutions of the natural residues with trp. Affinity of antagonists was further increased by replacing Met11 with either Nle or Phe. These new compounds showed some selectivity, [pro4, trp7’9, Nleπ]-SP (4–11) being more potent in the rabbit mesenteric vein than all other octapeptides described in the present study; on the other hand, [pro4, trp7’9’10, Phe11]-SP (4–11) was found to be the most potent antagonist of SP and related peptides in the guinea pig ileum and the guinea pig trachea. Both compounds were similarly active in the dog carotid artery. Undecapeptide antagonists, bearing the same structural modifications as the octapeptides, were found to be stimulant in the guinea pig trachea and relaxant in the dog carotid artery. The agonistic property was eliminated by repeated applications of the compounds in guinea pig tracheae, and therefore the compounds could be tested as antagonists. The undecapeptides were found to be much more active antagonists against kassinin and eledoisin than against SP and physalaemin. The data obtained with the octa and undecapeptide antagonists of SP have been used for identification and characterization of SP receptors in various smooth muscles. It appears that SP and related peptides may exert their numerous pharmacological effects by activating more than one receptor type.
Grassmannian Frames with Applications to Coding and Communication (2003)

For a given class ${\cal F}$ of uniform frames of fixed redundancy we define a Grassmannian frame as one that minimizes the maximal correlation $|< f_k,f_l >|$ among all frames $\{f_k\}_{k \in {\cal I}} \in {\cal F}$. We first analyze finite-dimensional Grassmannian frames. Using links to packings in Grassmannian spaces and antipodal spherical codes we derive bounds on the minimal achievable correlation for Grassmannian frames. These bounds yield a simple condition under which Grassmannian frames coincide with uniform tight frames. We exploit connections to graph theory, equiangular line sets, and coding theory in order to derive explicit constructions of Grassmannian frames. Our findings extend recent results on uniform tight frames. We then introduce infinite-dimensional Grassmannian frames and analyze their connection to uniform tight frames for frames which are generated by group-like unitary systems. We derive an example of a Grassmannian Gabor frame by using connections to sphere packing theory. Finally we discuss the application of Grassmannian frames to wireless communication and to multiple description coding.
Human embryonic stem cell-derived cardiac progenitors for severe heart failure treatment: first clinical case report: Figure 1 (2015)

This observation demonstrates the feasibility of generating a clinical-grade population of human ESC-derived cardiac progenitors and combining it within a tissue-engineered construct. While any conclusion pertaining to efficacy would be meaningless, the patient's functional outcome yet provides an encouraging hint. Beyond this case, the platform that has been set could be useful for generating different ESC-derived lineage-specific progenies.
Improved resolution with microchip‐based enhanced field inversion electrophoresis (2003)

We present an improvement of the field inversion electrophoresis (FIE) method in which the passage of sample such as DNA back and forth within a short length of a microchannel can provide a similar resolution to that of a significantly longer microchannel. In constant field FIE the application of an alternating potential (e.g., +/- V) over short periods of time (e.g., several Hz) can provide enhanced separations of DNA fragments. In contrast, the present method consists of a series of separations, each of much longer duration, under high and low fields in such a way that the resolution is enhanced. This method is readily modeled and allows improved resolution to be obtained from extremely short microchannels (e.g., 8 mm) while requiring relatively low applied voltages (e.g., less than 600 V). An additional advantage is that this method can allow for the same equipment to be used in a rapid, low-resolution mode or in a slower, high-resolution mode through what might be referred to as an automated "zoom" capability. We believe that this method may facilitate the integration of microfluidic devices and microelectronic devices by allowing these devices to be of a similar small scale (< 1 cm).
An endpoint associated with clinical benefit after initial treatment of chronic graft-versus-host disease (2017)

No gold standard has been established as a primary endpoint in trials of initial treatment of chronic graft-versus-host disease (GVHD), and evidence showing the association of any proposed primary endpoint with clinical benefit has not been conclusively demonstrated. To address this gap, we analyzed outcomes in a cohort of 328 patients enrolled in a prospective, multicenter, observational study within 3 months after diagnosis of chronic GVHD. Complete and partial response, stable disease, and progressive disease were defined according to the 2014 National Institutes of Health Consensus Development Conference on Criteria for Clinical Trials in Chronic Graft-Versus-Host Disease. Success was defined as complete or partial response with no secondary systemic treatment or recurrent malignancy at 1 year after enrollment. Success was observed in fewer than 20% of the patients. The burden of disease manifestations at 1 year was lower for patients in this category than for those with stable or progressive disease. Systemic treatment ended earlier, and subsequent mortality was lower among patients with complete or partial response than among those with stable or progressive disease and those who had received secondary systemic treatment. We conclude that survival with a complete or partial response and no previous secondary systemic treatment or recurrent malignancy at 1 year after initial systemic therapy is associated with clinical benefit, a critical characteristic for consideration as a primary endpoint in a pivotal clinical trial. This prospective observational study was registered at www.clinicaltrials.gov as #NCT00637689.
Mesenchymal stem cell interaction with a non‐woven hyaluronan‐based scaffold suitable for tissue repair (2008)

The fabrication of biodegradable 3-D scaffolds enriched with multipotent stem cells seems to be a promising strategy for the repair of irreversibly injured tissues. The fine mechanisms of the interaction of rat mesenchymal stem cells (rMSCs) with a hyaluronan-based scaffold, i.e. HYAFF(R)11, were investigated to evaluate the potential clinical application of this kind of engineered construct. rMSCs were seeded (2 x 10(6) cells cm(-2)) on the scaffold, cultured up to 21 days and analysed using appropriate techniques. Light (LM), scanning (SEM) and transmission (TEM) electron microscopy of untreated scaffold samples showed that scaffolds have a highly porous structure and are composed of 15-microm-thick microfibres having a rough surface. As detected by trypan blue stain, cell adhesion was high at day 1. rMSCs were viable up to 14 days as shown by CFDA assay and proliferated steadily on the scaffold as revealed by MTT assay. LM showed rMSCs in the innermost portions of the scaffold at day 3. SEM revealed a subconfluent cell monolayer covering 40 +/- 10% of the scaffold surface at day 21. TEM of early culture showed rMSCs wrapping individual fibres with regularly spaced focal contacts, whereas confocal microscopy showed polarized expression of CD44 hyaluronan receptor; TEM of 14-day cultures evidenced fibronexus formation. Immunohistochemistry of 21-day cultures showed that fibronectin was the main matrix protein secreted in the extracellular space; decorin and versican were seen in the cell cytoplasm only and type IV collagen was minimally expressed. The expression of CD90, a marker of mesenchymal stemness, was found unaffected at the end of cell culture. Our results show that HYAFF(R)11 scaffolds support the adhesion, migration and proliferation of rMSCs, as well as the synthesis and delivery of extracellular matrix components under static culture conditions without any chemical induction. The high retention rate and viability of the seeded cells as well as their fine modality of interaction with the substrate suggest that such scaffolds could be potentially useful when wide tissue defects are to be repaired as in the case of cartilage repair, wound healing and large vessel replacement.
Defective glucose counterregulation limits intensive therapy of diabetes mellitus (1984)

Defective recovery from insulin-induced hypoglycemia, due to combined deficiencies of glucagon and epinephrine secretory responses to plasma glucose decrements, occurs in some patients with insulin-dependent diabetes mellitus (IDDM). Patients with IDDM determined to have inadequate glucose counterregulation during an insulin infusion test (40 mU X kg-1 X h-1) with bedside plasma glucose monitoring and clinical observation have been found to have a 25-fold greater risk of severe hypoglycemia during subsequent intensive therapy than patients with adequate glucose counterregulation. Thus, the efficacy of the glucose counterregulatory systems determines the limits of intensive therapy of IDDM.
A Solid-State Electrode for Reducible Gases (1973)

The electrical properties of solid‐state electrochemical cells using thin‐film lanthanum fluoride electrolyte have been investigated as a function of the ambient atmosphere. The conductivity of the cells has been found to increase with the concentration of the reducible gases O2, , , , and . Sensitivity to a given gas is observed when the cell's terminal voltage exceeds a "characteristic potential" which correlates with the electron affinity of the gas. With suitable choice of anode material a galvanic cell is formed which may be used as a "self‐energized" O2 electrode or as a low current battery or O2 fuel cell.
Molecular organization of heat-labile enterotoxin genes originating in Escherichia coli of human origin and construction of heat-labile toxoid-producing strains (1981)

Recombinant deoxyribonucleic acid technology was employed to construct heat-labile enterotoxin (LT) toxoids. A recombinant plasmid carrying both an LT promoter region and LT subunit A (LTA) gene, lacking as much as 0.25 kilobases of the region up to the C terminus, produced a peptide possessing immunological properties of LTA but lacking the ability to construct LT activity (designated as LTA*). A cloned LT subunit B (LTB) gene produced LTB when a promoter on a vector was available for the gene. Escherichia coli producing LTA* and LTB (LT toxoids) could be useful as a vaccine.
Swap and Play (2014)

Hypervisors provide the means to run multiple isolated virtual machines on the same physical host. Typically, updating hypervisors requires a reboot of the host leading to disruption of services that is highly undesirable, particularly in cloud environments. Nevertheless, security updates have to be applied fast to reduce the risk of attacks, demanding a solution which eliminates the trade-off between availability and security risk.
Correlation of G/sub m/ degradation of submicrometer MOSFETs with refractive index and mechanical stress of encapsulation materials (1989)

Evaluations of five different plasma-deposited silicon nitride films for use as an encapsulation material for polysilicon-gate MOSFETs are discussed. The films were (1) a-SiN:H; (2) Applied Materials a-SiN:H process B; (3) Applied Materials a-SiN:H process D; (4) silicon oxynitride, a-SiON:H; and (5) fluorinated silicon nitride, a-SiNF:H. Submicrometer MOSFET devices that aged the least as measured by transconductance degradation were encapsulated with films having the lowest refractive index (a-SiON:H and a-SiNF:H). The results show that films with low refractive index and low absolute value of mechanical stress age the least. The results are interpreted in terms of the Meyer-Fair model where the lower refractive index films are more porous to H leaving the device than the higher refractive index films.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Two-photon absorption with exciton effect for degenerate valence bands (1974)

Two-photon absorption is treated theoretically using second-order perturbation theory. The exciton effect is taken into account for a crystal with degenerate valence bands. Calculations are made also including another energy band besides the conduction and valence bands. Expressions are given for the absorption of photon pairs from one radiation field and for the absorption of two photons, one from each of two different radiations. Experimental studies are made on ZnTe, GaAs, InP, and InSb. A Nd-glass laser is used for the measurements for ZnTe, GaAs, and InP; measurements on GaAs and InP are also made with the laser in combination with a Hg lamp. InSb is measured with a C${\mathrm{O}}_{2}$ laser. The experimental results are in good agreement with the calculations which take into account the exciton effect for degenerate valence bands, provided the two-photon energy is not too much larger than the energy gap. Calculations show that the degeneracy of valence band is important and that the importance of the exciton effect is larger the bigger the ratio of exciton binding energy to the difference between two-photon energy and the energy gap. These considerations are supported by the experimental results.
Temperature measurements during phacoemulsification and erbium:YAG laser phacoablation in model systems (1996)

At operating parameters sufficient for lens removal, the Er:YAG laser imparted less thermal energy to whole eyes and model systems than ultrasonic phacoemulsification.
FPGA Implementation of Orthogonal 2D Digital Predistortion System for Concurrent Dual-Band Power Amplifiers Based on Time-Division Multiplexing (2013)

A concurrent dual-band digital predistortion (DPD) system is presented to compensate for the nonlinearity of the radio-frequency power amplifiers (PAs) driven by a concurrent dual-band signal. Recently, a closed-form orthogonal polynomial basis has been introduced showing stability improvement compared with the conventional polynomial. An experimental test bed employing a field-programmable gate array (FPGA) linked to two mixed-signal system boards has also been presented. Based on the FPGA, this paper focuses on the hardware implementation of the new concurrent dual-band orthogonal DPD forward path using time-division multiplexing. Performances are evaluated with an experimental test setup cascading 1-10 W peak PAs and a dual-band signal center frequency spaced by 310 MHz. The lower side band (LSB) and upper side band (USB) are centered at 1890 and at 2200 MHz, respectively. Two signal scenarios are presented combining alternatively 1-carrier wide-band code-division multiple access (WCDMA) and 10-MHz long-term evolution (LTE) signals to a 5-carrier WCDMA signal. Experimental results show that the proposed time-division-multiplexing implementation approach gives similar performance compared with the software implementation with half of the resources. Adjacent channel power ratios (ACPRs) are reduced below -50 dBc and normalized mean-square error (NMSE) close to -40 dB.
Antibody-directed myostatin inhibition enhances muscle mass and function in tumor-bearing mice (2011)

Cancer cachexia describes the progressive skeletal muscle wasting and weakness in many cancer patients and accounts for >20% of cancer-related deaths. We tested the hypothesis that antibody-directed myostatin inhibition would attenuate the atrophy and loss of function in muscles of tumor-bearing mice. Twelve-week-old C57BL/6 mice received a subcutaneous injection of saline (control) or Lewis lung carcinoma (LLC) tumor cells. One week later, mice received either once weekly injections of saline (control, n = 12; LLC, n = 9) or a mouse chimera of anti-human myostatin antibody (PF-354, 10 mg·kg⁻¹·wk⁻¹, LLC+PF-354, n = 11) for 5 wk. Injection of LLC cells reduced muscle mass and maximum force of tibialis anterior (TA) muscles by 8-10% (P < 0.05), but the muscle atrophy and weakness were prevented with PF-354 treatment (P > 0.05). Maximum specific (normalized) force of diaphragm muscle strips was reduced with LLC injection (P < 0.05) but was not improved with PF-354 treatment (P > 0.05). PF-354 enhanced activity of oxidative enzymes in TA and diaphragm muscles of tumor-bearing mice by 118% and 89%, respectively (P < 0.05). Compared with controls, apoptosis that was not of myofibrillar or satellite cell origin was 140% higher in TA muscle cross sections from saline-treated LLC tumor-bearing mice (P < 0.05) but was not different in PF-354-treated tumor-bearing mice (P > 0.05). Antibody-directed myostatin inhibition attenuated the skeletal muscle atrophy and loss of muscle force-producing capacity in a murine model of cancer cachexia, in part by reducing apoptosis. The improvements in limb muscle mass and function highlight the therapeutic potential of antibody-directed myostatin inhibition for cancer cachexia.