gebhart/patrepeval huggingface dataset:
Immunohistochemical localization of glutathione-S-transferase and glutathione peroxidase in adult Syrian hamster tissues and during kidney development. (1991)

Tissues from adult Syrian hamsters were studied with immunoperoxidase techniques using polyclonal antibodies to glutathione-S-transferase (rat liver and human placental enzymes) and human erythrocyte glutathione peroxidase. Most tissues immunostained similarly with these antibodies. Most notable was the cytoplasmic staining of mesenchyme tissues, especially smooth muscle, by all three antibodies. Epithelial cells stained distinctively, but usually less intensely than mesenchyme. Epithelial cells from all levels of the gastrointestinal tract, respiratory epithelium, transitional epithelium, and epidermis all showed strong staining with these antibodies. Other epithelial cell types were usually positive but showed less dramatic staining. Most epithelial tissues showed both nuclear and cytoplasmic staining; some also showed cell-surface (eg, cilia) staining. The role of these enzymes in cell differentiation of a stable organ was studied by immunostaining the kidney during its development. Early stroma (13- and 15-day fetuses) of the kidney (metanephric mesenchyme) showed strong cell-surface staining for glutathione transferases and moderate staining for glutathione peroxidase; renal tubules (which are epithelial cells) at this stage were negative for these markers. As renal tubules differentiated, first cytoplasm and then nuclei stained moderately, suggesting that glutathione-S-transferases and glutathione peroxidase are markers of both mesenchymal cells, including embryonic mesenchyme, and terminal differentiation of at least some epithelial cells.
Auto-WEKA: Automatic Model Selection and Hyperparameter Optimization in WEKA (2019)

Many different machine learning algorithms exist; taking into account each algorithm’s hyperparameters, there is a staggeringly large number of possible alternatives overall. We consider the problem of simultaneously selecting a learning algorithm and setting its hyperparameters. We show that this problem can be addressed by a fully automated approach, leveraging recent innovations in Bayesian optimization. Specifically, we consider feature selection techniques and all machine learning approaches implemented in WEKA’s standard distribution, spanning 2 ensemble methods, 10 meta-methods, 28 base learners, and hyperparameter settings for each learner. On each of 21 popular datasets from the UCI repository, the KDD Cup 09, variants of the MNIST dataset and CIFAR-10, we show performance often much better than using standard selection and hyperparameter optimization methods. We hope that our approach will help non-expert users to more effectively identify machine learning algorithms and hyperparameter settings appropriate to their applications, and hence to achieve improved performance.
Mild Copper‐Catalyzed Fluorination of Alkyl Triflates with Potassium Fluoride (2014)

A chemoselective catalytic fluorination of alkyl triflates is described using potassium fluoride as a fluoride source. Excellent yields of the desired alkyl fluorides are obtained after one hour at 45 °C using 2 mol% of the copper catalyst. With 10 mol% of the catalyst, full conversion can be achieved in less than 10 minutes at 45 °C, and thus makes this procedure potentially suited for the preparation of (18) F-labeled PET probes. As a result of the mild reaction conditions, only the substitution products are observed with no evidence of common side reactions, such as elimination. Reported is a preliminary study of the reaction scope, which demonstrates that the fluorination can be performed in the presence of a wide range of functional groups. Evidence suggests an unusual role of the [IPrCuOTf] catalyst as a phase-transfer catalyst and points to [IPrCuF] as the active fluorinating reagent (IPr=1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene).
Species-Dependent Pharmacological Properties of the Melanocortin-5 Receptor (2000)

The genes encoding the melanocortin-3 receptor and melanocortin-5 receptor have been cloned from rhesus monkey. Heterologous expression in CHO cells indicated species dependent in vitro pharmacological properties for the human and rhesus melanocortin-5 receptors. Several peptides including NDP-alpha-MSH, alpha-MSH, MT-II and ACTH1-24 are more potent at the rhesus melanocortin-5 receptor than the human melanocortin-5 receptor by more than 10-fold. In contrast, we found no species difference in pharmacological properties between the human and rhesus melanocortin-3 receptors. Such a species-dependent pharmacological difference for melanocortin-5 receptor appears to be an exception compared to other G protein-coupled receptors from human and rhesus monkey.
Tissue Engineering of a Bioartificial Renal Tubule (1998)

Development of a bioartificial renal tubule with a confluent monolayer of renal epithelial cells supported on a permeable synthetic surface may be the first step to further optimization of renal substitution therapy currently used with hemodialysis or hemofiltration. Madin-Darby canine kidney cells, a permanent renal epithelial cell line, were seeded into the lumen of single hollow fibers. Functional confluence of the cells was demonstrated by the recovery of intraluminally perfused 14C-inulin that averaged >98.9% in the cell lined units vs <7.4% in the control noncell hollow fibers during identical pressure and flow conditions. The baseline absolute fluid transport rate averaged 1.4+/-0.4 microl/30 min. To test the dependency of fluid flux with oncotic and osmotic pressure differences across the bioartificial tubule, albumin was added to the extracapillary space, followed by the addition of ouabain, an inhibitor of Na+K+ adenosine triphosphatase, the enzyme responsible for active transport across the renal epithelium. Addition of albumin resulted in a significant increase in volume transport to 4.5+/-1.0 microl/30 min. Addition of ouabain inhibited transport back to baseline levels of 2.1+/-0.4 microl/30 min. These results are the first demonstration that renal epithelial cells have been grown successfully as a confluent monolayer along a hollow fiber, and exhibit functional transport capabilities. The next steps in constructing a bioartificial renal tubule successfully are to develop a multi-fiber bioreactor with primary renal proximal tubule cells that maintain not only transport properties but also differentiated metabolic and endocrine functions, including glucose and ammonia production, and the conversion of vitamin D3 to a more active derivative. A renal tubule device may add critical renal functional components not currently substituted for, thereby improving the treatment regimens for patients with acute and chronic renal failure.
Monoterpenoid agonists of TRPV3 (2007)

Terpenoids have long been recognized as medically and pharmacologically active compounds, although their molecular targets have only partially been identified. TRPV3 activation may be responsible for several of the described effects of terpenoids. We show here that TRPV3 is activated by a number of monoterpenes and that a secondary hydroxyl-group is a structural requirement.
Kinetic analysis of T7 RNA polymerase-promoter interactions with small synthetic promoters (1987)

Specific interactions between T7 RNA polymerase and its promoter have been studied by a simple steady-state kinetic assay using synthetic oligonucleotide promoters that produce a short five-base message. A series of promoters with upstream lengths extending to promoter positions -19, -17, -14, and -12 show that promoters extending to -19 and -17 produce very specific transcripts with initiation rate constant Kcat = 50 min-1 and a Michaelis constant Km = 0.02 microM, indicating that the consensus sequence to position -17 is sufficient for maximum promoter usage. Shortening the upstream region of the promoter to -14 substantially increases Km (0.3 microM) but does not significantly reduce the maximum velocity (kcat = 30 min-1). Finally, truncation of the promoter at position -12 results in extremely low levels of specific transcription. The coding and noncoding strands appear to make different contributions to promoter recognition. Although the double-stranded promoter of upstream length -12 is very poor as a transcription template, extension of only the noncoding strand to -17 very significantly improves both Kcat and Km. In contrast, extension of only the coding strand results in no significant improvement. Substitution of an AT base pair at position -10 by CG (as found in T3 RNA polymerase promoters) produces a 10-fold increase in Km, with little effect on Kcat. Comparison of two promoters containing a base pair mismatch at this site (AG or CT) demonstrates that promoter recognition is very sensitive to the nature of the base on the noncoding strand and is only slightly affected by the presence of a mismatch created by a wrong base in the coding strands.(ABSTRACT TRUNCATED AT 250 WORDS)
Fault tolerant networks of workstations (2002)

Networks of workstations make cheap and powerful parallel processors and many systems have been demonstrated using Unix workstations. Personal computers, with their cheap, high performance CPUs, can also be used in a similar way. However, if we are to exploit the multitudes of PCs that sit on desks idle for much of the time, we need robust systems. The uncontrolled environment and physical separation between elements of the parallel system make them prone to a variety of faults that would not normally plague a single processor in a machine room. We describe extensions made to the run-time system for Old MacDonald-a network of PowerPC based Macintoshes-to enable programs written in a functional style using Cilk-a threaded extension of C-to continue in the face of processor and network failures and unpredictable delays likely to be encountered when using widely dispersed machines as components of a parallel system.
Protein Purification, and Cloning and Characterization of the cDNA and Gene for Xylose Isomerase of Barley (1996)

The first eukaryotic xylose isomerase protein was purified from barley Hordeum vulgare. The enzyme requires Mn2+ for its activity and is fairly thermostable, with the optimum temperature being 60 degrees C. It showed maximum activity over a broad pH range (7.0-9.0). The molecular mass of the monomer was about 50,000 Da based on the SDS/PAGE, and the calculated value from the cDNA-deduced polypeptide sequence was 53,620 Da. A relative mass estimation of 100,000 Da was obtained from the Superose 12 chromatography, suggesting that the barley enzyme is a dimer. The cloned corresponding cDNA sequence of 1710 nucleotides encoded a polypeptide of 480 amino acids. The genomic sequence of 4473 nucleotides, revealed that the isomerase gene contained 20 introns, all starting with GT and ending with AG. One large intron was located in the 5'untranslated region. The barley isomerase has an insertion of about 40 residues at its amino terminus when compared to the prokaryotic cluster (family) II isomerases; cluster (family) I and cluster (family) II isomerases vary from the former in an insertion of around 50 residues at their amino termini. Comparison of the barley protein with the prokaryotic isomerases shows that the conserved catalytic and metal binding regions are also well conserved in barley.
Activation and Function of the mTORC1 Pathway in Mast Cells (2008)

Little is known about the signals downstream of PI3K which regulate mast cell homeostasis and function following FcepsilonRI aggregation and Kit ligation. In this study, we investigated the role of the mammalian target of rapamycin complex 1 (mTORC1) pathway in these responses. In human and mouse mast cells, stimulation via FcepsilonRI or Kit resulted in a marked PI3K-dependent activation of the mTORC1 pathway, as revealed by the wortmannin-sensitive sequential phosphorylation of tuberin, mTOR, p70S6 kinase (p70S6K), and 4E-BP1. In contrast, in human tumor mast cells, the mTORC1 pathway was constitutively activated and this was associated with markedly elevated levels of mTORC1 pathway components. Rapamycin, a specific inhibitor of mTORC1, selectively and completely blocked the FcepsilonRI- and Kit-induced mTORC1-dependent p70S6K phosphorylation and partially blocked the 4E-BP1 phosphorylation. In parallel, although rapamycin had no effect on FcepsilonRI-mediated degranulation or Kit-mediated cell adhesion, it inhibited cytokine production, and kit-mediated chemotaxis and cell survival. Furthermore, Rapamycin also blocked the constitutive activation of the mTORC1 pathway and inhibited cell survival of tumor mast cells. These data provide evidence that mTORC1 is a point of divergency for the PI3K-regulated downstream events of FcepsilonRI and Kit for the selective regulation of mast cell functions. Specifically, the mTORC1 pathway may play a critical role in normal and dysregulated control of mast cell homeostasis.
Laboratory and epidemiologic evaluation of an enzyme immunoassay for antibodies to HTLV-III (1986)

The enzyme immunoassays (ElAs) for antibody to human T-cell lymphotropic virus type III (HTLV-III) were rapidly adopted for screening donated blood and plasma. To evaluate the significance of a positive EIA reaction, test performance was examined in a blood bank screening program. Specimens were tested by EIA, Western blot assay, and HTLV-III/ lymphadenopathyassociated virus (LAV) culture. The EIA was positive in 0.25% of 67 190 blood donations. Specimens were categorized and 57.3% had low (weak) reactivity, 12.7% had moderate reactivity, and 30.0% had high reactivity. Highly reactive specimens were strongly associated with a positive Western blot or culture (86.7%) in contrast to moderately and weakly reactive specimens (1.9%). Twenty-five of 29 donors interviewed with a highly reactive EIA had risk factors for HTLV-III/LAV infection. Risk factors were not identified for 74 of 75 interviewed donors with specimens of lower reactivity. The minimum calculated specificity was 99.82%. The use of the HTLV-III EIA has virtually eliminated the use of blood and plasma from HTLV-III/LAV infected donors. (<i>JAMA</i>1986;256:357-361)
Human endothelial cell interactions with surface‐coupled adhesion peptides on a nonadhesive glass substrate and two polymeric biomaterials (1991)

The attachment, spreading, spreading rate, focal contact formation, and cytoskeletal organization of human umbilical vein endothelial cells (HUVECs) were investigated on substrates that had been covalently grafted with the cell adhesion peptides Arg-Gly-Asp (RGD) and Tyr-Ile-Gly-Ser-Arg (YIGSR). This approach was used to provide substrates that were adhesive to cells even in the absence of serum proteins and with no prior pretreatment of the surface with proteins of the cell adhesion molecule (CAM) family. This approach was used to dramatically enhance the cell-adhesiveness of substrates that were otherwise cell-nonadhesive and to improve control of cellular interactions with cell-adhesive materials by providing stably bound adhesion ligands. Glycophase glass was examined as a model cell-nonadhesive substrate prior to modification, and polyethylene terephthalate (PET) and polytetrafluoroethylene (PTFE) were examined as representative materials for biomedical applications. The peptides were surface-coupled by their N-terminal amine to surface hydroxyl moieties using tresyl chloride chemistry. Prior to peptide grafting, the PET and PTFE were surface hydroxylated to yield PET-OH and PTFE-OH. The PET-OH was less cell-adhesive and the PTFE-OH was much more cell-adhesive than the native polymers. Radioiodination of a C-terminal tyrosine residue was used to quantify the amount of peptide coupled to the surface, and these amounts were 12.1 pmol/cm2 on glycophase glass, 139 fmol/cm2 on PET-OH, and 31 fmol/cm2 on PTFE-OH. Although the glycophase glass did not support adhesion or spreading even in the presence of serum, the RGD- and YIGSR-grafted glycophase glass did support adhesion and spreading, even when the only serum protein that was included was albumin. Although PET and PTFE-OH supported adhesion when incubated in serum-supplemented medium, neither of these materials supported adhesion with only albumin present, indicating that cell adhesion is mediated by adsorbed CAM proteins. When these materials were peptide-grafted, however, extensive adhesion and spreading did occur even when only albumin was present. Since the peptide grafting is quite easily controlled and is temporally stable, while protein adsorption is quite difficult to precisely control and is temporally dynamic, peptide grafting may be advantageous over other approaches employed to improve long-term cell adhesion to biomaterials.
Use of homologous platelet factors in achieving total healing of recalcitrant skin ulcers. (1990)

We used homologous platelet-derived wound healing factors (HPDWHF) to achieve complete healing of recalcitrant ulcers of diverse cause. Twenty-three patients with 27 skin ulcers who had been receiving conventional wound care with no evidence of healing for an average period of 25 weeks (range, 12 to 156 weeks) were studied. The patients were first subjected to controlled wound care for 3 months, with saline solution and silver sulfadiazine dressings used in all cases. At the end of this period, persistent nonhealing ulcers were treated by topical use of HPDWHF and silver sulfadiazine. Ulcer parameters were recorded on the first day and every week during therapy until complete epithelization was achieved in either group. Each ulcer acted as its own control. In the controlled wound care group, only three ulcers in three patients achieved complete healing; the remaining 24 ulcers in 20 patients failed to achieve even 50% healing in the stipulated 3-month period. However, when subjected to HPDWHF applications, these ulcers healed completely, 100% healing occurring in 9.67 +/- 4.9 weeks (range, 3 to 19 weeks), which is highly significant (p less than 0.01). The healing response to HPDWHF applications was of uniform progression over the weeks. Only the basic cause of the ulcer determined the healing rates in this group. The shortest and the longest time to achieve 100% healing occurred in patients with diabetes (6.88 +/- 2.97 weeks) and in the venous stasis group (14.00 +/- 7.07 weeks). Age, sex, location of ulcer, ulcer duration, and ulcer measurements had no influence on the HPDWHF-stimulated healing rates. This is the earliest report of HPDWHF-stimulated repair in chronic nonhealing skin ulcers.
Cyclometalated Platinum(II) Complexes of Pyrazole-Based, N∧C∧N-Coordinating, Terdentate Ligands: the Contrasting Influence of Pyrazolyl and Pyridyl Rings on Luminescence (2008)

1,3-Bis(1-pyrazolyl)-5-methyl-benzene, HL(2), undergoes cyclometalation at the C(2) position upon reaction with K(2)PtCl(4), to generate an N=C=N-coordinated complex, PtL(2)Cl. This compound is luminescent in degassed solution at 298 K, emitting in the blue region of the spectrum on the microsecond time scale (lambda(max) = 453 nm, tau = 4.0 micros, Phi(lum) = 0.02, in CH(2)Cl(2)). Compared to the analogous complex Pt(dpyb)Cl that incorporates pyridyl rather than pyrazole rings {dpybH = 1,3-di(2-pyridyl)-benzene}, the excited state is displaced to higher energy by 1700 cm(-1). This effect is rationalized in terms of the poorer pi-acceptor nature of pyrazolyl compared to pyridyl rings, leading to destabilization of the lowest unoccupied molecular orbital, which is largely localized on the heteroaromatic rings in both cases. Cyclic voltammetry and density functional theory calculations reinforce this interpretation, and suggest that the lowest-energy excited state is probably best described as heavily mixed pi(L)/d(Pt)/p(Cl) --> pi*(L) (IL/MLCT/LLCT) in character. 5-Aryl-substituted analogues of HL(2) are accessible in three steps from 1,3,5-tribromobenzene by Pd-catalyzed cross-coupling with aryl boronic acids, followed by copper-catalyzed bromo-iodo exchange, and subsequent amination with pyrazole under relatively mild conditions also catalyzed by copper. The corresponding Pt(II) complexes display red-shifted and more intense luminescence compared to PtL(2)Cl. Ligands incorporating one pyrazole and one pyridyl ring are also accessible; for example, 1-(1-pyrazolyl)-3-(2-pyridyl)benzene, HL(6). Their complexes are highly luminescent in solution; for example, for PtL(6)Cl, lambda(max) = 487 nm, tau = 6.9 micros, Phi(lum) = 0.55, in dilute solution in CH(2)Cl(2). At elevated concentrations, PtL(6)Cl displays an additional excimeric emission band that is substantially blue-shifted compared to that displayed by Pt(dpyb)Cl (bands centered at 645 and 695 nm, respectively), indicating that the presence of the pyrazole ring destabilizes the excimer. The introduction of a methyl substituent into the central aryl ring of such complexes is sufficient to eliminate the excimer emission.
Calcium chloride in neonatal parenteral nutrition: A 15 year experience (2017)

The use of CaCl2 was not associated with any detectable adverse effects. Calcium chloride appears to be a safe alternative to the use of CaGlu-Gl based upon studies of clinical outcomes.
Notch1 activation increases hematopoietic stem cell self-renewal in vivo and favors lymphoid over myeloid lineage outcome (2002)

Hematopoietic stem cells sequentially pass through a series of decision points affecting self-renewal or lineage-specific differentiation. Notch1 receptor is a known modulator of lineage-specific events in hematopoiesis that we assessed in the context of in vivo stem cell kinetics. Using RAG-1(-/-) mouse stems cells, we documented increased stem cell numbers due to decreased differentiation and enhanced stem cell self-renewal induced by Notch1. Unexpectedly, preferential lymphoid over myeloid lineage commitment was noted when differentiation occurred. Therefore, Notch1 affects 2 decision points in stem cell regulation, favoring self-renewal over differentiation and lymphoid over myeloid lineage outcome. Notch1 offers an attractive target for stem cell manipulation strategies, particularly in the context of immunodeficiency and acquired immunodeficiency syndrome.