gebhart/patrepeval huggingface dataset:
3D packaging: where all technologies come together (2004)

Cell phones and consumer products like digital cameras, PDAs and other wireless devices require maximum functional integration in the smallest footprint, lowest profile and low cost package. CSPs have minimized the footprint to achieve a chip/package area ratio about 80%. 3D packaging has increased that ratio to the impressive level of > 200% without increasing the thickness or the footprint of the package. Integration in the z-direction is achieved by stacking die or stacking packages and interconnecting them with wire bonding. 3D packages are assembled using the established packaging infrastructure and supply chain which offers design flexibility, short time-to-market, low risk and low cost product introduction. 3D packaging poses two challenges. First, the stacking of more chips in a thinner package stretches the performance envelope of all assembly process, materials and equipment. Narrower process margins, thin layer materials, equipment with higher precision and flexibility require trade-offs to minimize risk and cost without compromising the reliability of the package. Second, the testing of the final module requires that package design allow access to all the chips. Integration of complex chips from multiple suppliers in one package creates a high value module and increased test complexity.
The effects of lipid composition on the rate and extent of heme binding to membranes. (1990)

The effects of membrane composition on heme binding to large unilamellar vesicles were examined using 30 separate phospholipid mixtures. Although there was some variation, most lecithins with Tm values less than or equal to 20 degrees C showed overall equilibrium partition constants equal to approximately 5 x 10(5) and association and dissociation partition rate constants equal to approximately 3 x 10(6) s-1 and 7 s-1, respectively, for CO-heme binding at 30 degrees C. A sharp decrease in the association rate for CO-heme uptake was observed as the lipid vesicles changed from liquid-crystalline to the gel phase. The addition of dicetyl phosphate or dimyristoylphosphatidylglycerol, which are negatively charged at neutral pH, decreased the affinity of the vesicles for CO-heme. The association rate and equilibrium partition constants for CO-heme uptake in unsaturated lecithins were unaffected by cholesterol content at levels up to 40%/mol. The affinity of saturated dimyristoylphosphatidylcholine (DMPC) vesicles for CO-heme decreased with increasing cholesterol content at 30 degrees C. This effect appears to be related to the influence of cholesterol on the DMPC phase transition temperature (Tm) since at low temperatures (less than or equal to 20 degrees C) little CO-heme binds to vesicles composed of DMPC even in the absence of cholesterol.
Lisinopril, an angiotensin I-converting enzyme inhibitor, prevents entry of murine hematopoietic stem cells into the cell cycle after irradiation in vivo. (1998)

The hemoregulatory peptide N-Acetyl-Ser-Asp-Lys-Pro (AcSDKP) has been shown in vivo to inhibit the cycling of murine hematopoietic stem cells triggered into S-phase by either cytotoxic drug administration or irradiation. This property, further confirmed using in vitro models, demonstrates that the peptide has an in vivo protective effect on the hematopoietic system. AcSDKP has been shown to be a physiological substrate of angiotensin I-converting enzyme (ACE), which catabolizes the peptide through a dipeptidasic activity. Thus, oral administration of ACE inhibitor to humans has led to an increase in the plasma AcSDKP concentration. In the present paper, we report on the in vivo effect of lisinopril, an ACE inhibitor, on the proliferative status of murine hematopoietic stem cells triggered into S-phase by irradiation. Administration of lisinopril (10 mg/kg) 1 hour after irradiation led to a 90 to 100% inhibition of murine plasma ACE activity as observed during the first 4 hours postirradiation. This inhibition was correlated with a 600% increase in the endogenous plasma AcSDKP level and a total suppression at 24 hours of entry of the hematopoietic stem cell into the cell cycle. We discuss the possible role of ACE in the regulation of hematopoietic stem cell proliferation through control of the AcSDKP concentration.
Structure of a Peptide Inhibitor Bound to the Catalytic Subunit of Cyclic Adenosine Monophosphate-Dependent Protein Kinase (1991)

The structure of a 20-amino acid peptide inhibitor bound to the catalytic subunit of cyclic AMP-dependent protein kinase, and its interactions with the enzyme, are described. The x-ray crystal structure of the complex is the basis of the analysis. The peptide inhibitor, derived from a naturally occurring heat-stable protein kinase inhibitor, contains an amphipathic helix that is followed by a turn and an extended conformation. The extended region occupies the cleft between the two lobes of the enzyme and contains a five-residue consensus recognition sequence common to all substrates and peptide inhibitors of the catalytic subunit. The helical portion of the peptide binds to a hydrophobic groove and conveys high affinity binding. Loops from both domains converge at the active site and contribute to a network of conserved residues at the sites of magnesium adenosine triphosphate binding and catalysis. Amino acids associated with peptide recognition, nonconserved, extend over a large surface area.
An L-lactic acid dehydrogenase based method for detecting microbial colonies performing a malo-lactic fermentation (1982)

Microbial colonies capable of fermenting L-malic acid to L-lactic acid were identified by means of a dark blue halo which formed after the colonies had been grown on medium containing malic acid and then covered with a soft agar overlay containing L-lactic acid dehydrogenase, nicotinamide adenine dinucleotide, phenazine methosulfate, and nitro blue tetrazolium. The system is stereospecific and discriminates between the production of D-lactic and L-lactic acid. Chromatographic analysis of the medium adjacent to the colony distinguishes between those colonies producing L-lactate from L-malate and those producing DL-lactate from glucose. The system may be used to identify wine microbes capable of performing a malo-lactic fermentation, comparing two bacterial strains for their ability to perform a malo-lactic fermentation, and for the identification of clones of an organism carrying a recombinant DNA vector with the genetic material necessary for malo-lactic fermentation.
Fault-tolerant designs for 256 Mb DRAM (1996)

This paper describes fault-tolerant designs, which have been used to boost the yield of a 286 mm/sup 2/ 256 Mb DRAM with x32 both-ends DQ. The 256 Mb DRAM consists of sixteen 16 Mb units, each containing one 128 Kb row redundancy block. This row redundancy block architecture allows flexible row redundancy replacement, where random faults, clustered faults, and grouped faults can be efficiently repaired. Flexible column redundancy replacement with interchangeable master DQ's (MDQ) is used to allow a 256 b data compression without causing a data conflict, while improving the column access speed by 2 ns. A depletion NMOS bitline-precharge-current-limiter suppresses the current flow which occurs as a result of a wordline-bitline short-circuit to only 15 /spl mu/A per cross fail, avoiding a standby current fail. Consequently, the hardware results show a significant yield enhancement of 16 times relative to the intra-block/segment replacement. Detailed simulation results show that this 256 Mb DRAM allows 275 random faults to be repaired with 5.5% silicon area overhead for 80% chip yield.
Identification of Gene Expression Biomarkers for Predicting Radiation Exposure (2014)

A need for more accurate and reliable radiation dosimetry has become increasingly important due to the possibility of a large-scale radiation emergency resulting from terrorism or nuclear accidents. Although traditional approaches provide accurate measurements, such methods usually require tedious effort and at least two days to complete. Therefore, we provide a new method for rapid prediction of radiation exposure. Eleven microarray datasets were classified into two groups based on their radiation doses and utilized as the training samples. For the two groups, Student's t-tests and resampling tests were used to identify biomarkers, and their gene expression ratios were used to develop a prediction model. The performance of the model was evaluated in four independent datasets, and Ingenuity pathway analysis was performed to characterize the associated biological functions. Our meta-analysis identified 29 biomarkers, showing approximately 90% and 80% accuracy in the training and validation samples. Furthermore, the 29 genes significantly participated in the regulation of cell cycle, and 19 of them are regulated by three well-known radiation-modulated transcription factors: TP53, FOXM1 and ERBB2. In conclusion, this study demonstrates a reliable method for identifying biomarkers across independent studies and high and reproducible prediction accuracy was demonstrated in both internal and external datasets.
Engineered nanoparticles induce cell apoptosis: potential for cancer therapy (2016)

Engineered nanoparticles (ENPs) have been widely applied in industry, commodities, biology and medicine recently. The potential for many related threats to human health has been highlighted. ENPs with their sizes no larger than 100 nm are able to enter the human body and accumulate in organs such as brain, liver, lung, testes, etc, and cause toxic effects. Many references have studied ENP effects on the cells of different organs with related cell apoptosis noted. Understanding such pathways towards ENP induced apoptosis may aid in the design of effective cancer targeting ENP drugs. Such ENPs can either have a direct effect towards cancer cell apoptosis or can be used as drug delivery agents. Characteristics of ENPs, such as sizes, shape, forms, charges and surface modifications are all seen to play a role in determining their toxicity in target cells. Specific modifications of such characteristics can be applied to reduce ENP bioactivity and thus alleviate unwanted cytotoxicity, without affecting the intended function. This provides an opportunity to design ENPs with minimum toxicity to non-targeted cells.
Aptamers for pharmaceuticals and their application in environmental analytics (2011)

Aptamers are single-stranded DNA or RNA oligonucleotides, which are able to bind with high affinity and specificity to their target. This property is used for a multitude of applications, for instance as molecular recognition elements in biosensors and other assays. Biosensor application of aptamers offers the possibility for fast and easy detection of environmental relevant substances. Pharmaceutical residues, deriving from human or animal medical treatment, are found in surface, ground, and drinking water. At least the whole range of frequently administered drugs can be detected in noticeable concentrations. Biosensors and assays based on aptamers as specific recognition elements are very convenient for this application because aptamer development is possible for toxic targets. Commonly used biological receptors for biosensors like enzymes or antibodies are mostly unavailable for the detection of pharmaceuticals. This review describes the research activities of aptamer and sensor developments for pharmaceutical detection, with focus on environmental applications.
Relationship of Estrogen and Progesterone Receptors to Prognosis in Breast Cancer (1988)

To ascertain the role of estrogen (ER) and progesterone (PR) receptors as prognostic indicators of resectable breast cancer, the records of 204 patients were analyzed whose receptor studies were done at the Maimonides Medical Center from 1975 to 1983. All patients had radical or modified radical mastectomies and did not show any evidence of distant metastases at the time of operation. Median follow-up was 37 months. An additional 117 patients received some form of adjuvant therapy, mainly chemotherapy, and were analyzed separately. Life table analysis using the log rank test for measuring significance, and a Cox multivariate analysis was performed. At 48 months, 22% of the ER positive (ER+) group versus 33% of the ER negative (ER-) group had recurred as compared to 16% and 35% for the PR+ versus PR- groups, respectively. Life table analysis of the disease free interval (DFI) showed that the difference between the ER+ and ER- groups was not significant (p greater than 0.1), while the difference in DFI between the PR+ and PR- groups was significant (p less than 0.05). Multivariate analysis revealed that the most important factors in predicting the DFI were nodal status (p less than 0.001), tumor size (p less than 0.025), and progesterone receptor status (p less than 0.05). Estrogen receptor status was not found to be significant. In conclusion, PR- patients have a shorter DFI than PR+ patients and that PR status is a more valuable predictor of DFI than ER status.
Licochalcone A Inhibits the Growth of Colon Carcinoma and Attenuates Cisplatin‐Induced Toxicity without a Loss of Chemotherapeutic Efficacy in Mice (2008)

Although chemotherapy has an important function in the treatment of most solid tumours, its clinical applications are limited by severe side effects such as nephrotoxicity, hepatotoxicity, ototoxicity and neurotoxicity. Recently, a growing amount of attention has been focused on the investigation of the effects of chemopreventive agents on the inhibition of cancer cell growth and toxicity in combination with chemotherapeutics. The aim of this study was to determine whether licochalcone A (LCA) has the potential to serve as a beneficial supplement during cisplatin chemotherapy. We found that the administration of LCA alone significantly inhibited the size of the solid tumours in CT-26 cell-inoculated Balb/c mice, without any detectable induction of nephrotoxicity, hepatotoxicity and oxidative stress. LCA also suppressed cell proliferation by reducing DNA synthesis of CT-26 murine colon cancer cells in a dose-dependent manner. LCA did not affect the therapeutic efficacy of cisplatin. Furthermore, LCA inhibited the cisplatin-induced kidney damage characterized by increases in the serum creatinine and blood urea nitrogen, as well as the cisplatin-induced liver damage characterized by increases in the serum alanine aminotransferase and aspartate aminotransferase. The repeated oral administration of LCA prior to cisplatin treatment exerted a preventive effect on the cisplatin-mediated increases in the serum nitric oxide and the tissue lipid peroxidation levels, and recovered the depleted reduced glutathione levels in the tissues. These results suggest that supplementation with LCA may be beneficial in counteracting the side effects of cisplatin therapy in cancer patients.
Factor IX variants improve gene therapy efficacy for hemophilia B (2004)

Intramuscular injection of adeno-associated viral (AAV) vector to skeletal muscle of humans with hemophilia B is safe, but higher doses are required to achieve therapeutic factor IX (F.IX) levels. The efficacy of this approach is hampered by the retention of F.IX in muscle extracellular spaces and by the limiting capacity of muscle to synthesize fully active F.IX at high expression rates. To overcome these limitations, we constructed AAV vectors encoding F.IX variants for muscle- or liver-directed expression in hemophilia B mice. Circulating F.IX levels following intramuscular injection of AAV-F.IX-K5A/V10K, a variant with low-affinity to extracellular matrix, were 2-5 fold higher compared with wild-type (WT) F.IX, while the protein-specific activities remained similar. Expression of F.IX-R338A generated a protein with 2- or 6-fold higher specific activity than F.IX-WT following vector delivery to skeletal muscle or liver, respectively. F.IX-WT and variant forms provide effective hemostasis in vivo upon challenge by tail-clipping assay. Importantly, intramuscular injection of AAV-F.IX variants did not trigger antibody formation to F.IX in mice tolerant to F.IX-WT. These studies demonstrate that F.IX variants provide a promising strategy to improve the efficacy for a variety of gene-based therapies for hemophilia B.
Autoantigens interact with cis-acting elements of rubella virus RNA (1996)

Rubella virus (RV) infections in adult women can be associated with acute and chronic arthritic symptoms. In many autoimmune individuals, antibodies are found targeting endogenous proteins, called autoantigens, contained in ribonucleoprotein complexes (RNPs). In order to understand the molecular mechanisms involved in the RV-associated pathology, we investigated the nature of cellular factors binding RV RNA and whether such RNPs were recognized by antibodies in infected individuals. Previously, we noted that cellular proteins associated with the RV 5'(+) stem-loop (SL) RNA are recognized by serum with Ro reactivity. To better understand the nature of the autoantigens binding RV cis-acting elements, serum samples from individuals with various autoimmune diseases were tested for their ability to immunoprecipitate RNPs containing labeled RV RNAs. A subset of serum samples recognizing autoantigen La, or Ro and La, immunoprecipitated both the RV 5'(+)SL and 3'(+)SL RNA-protein complexes. Autoantigens binding the RV 5'(+)SL and 3'(+)SL RNAs differed in molecular mass, specificities for respective RNA binding substrates, and sensitivity to alkaline phosphatase treatment. The La autoantigen was found to interact with the RV 5'(+)SL RNA as determined by immunological techniques and binding reactions with mixtures containing recombinant La protein. To test whether there is a correlation between La binding to an RV RNA element and the appearance of an anti-La response, we measured anti-La titers in RV-infected individuals. Significant anti-La activity was detected in approximately one-third of RV-infected individuals 2 years postinfection.
Cyclodextrins as Drug Carrier Molecule: A Review (2008)

The cyclodextrins have a wide range of applications in different areas of drug delivery and pharmaceutical industry due to their complexation ability and other versatile characteristics. The most common pharmaceutical application of cyclodextrin is to enhance the solubility, stability, safety and bioavailability of drug molecules. The purpose of this review is to discuss and summarize some of the findings and applications of cyclodextrin (CD) and their derivatives in different areas of drug delivery. This article highlights the molecular structure, properties like complexation, solubility etc. of cyclodextrins and focuses on its use for parenteral, oral, ophthalmic and nasal drug delivery. Other routes including dermal, rectal, sublingual and pulmonary delivery are also briefly addressed. The objective of this contribution is to focus on the potential use of chemically modified cyclodextrins as high-performance drug carriers in drug delivery systems with emphasis on the more recent developments. Thus cyclodextrins, because of their continuing ability to find several novel applications in drug delivery, are expected to solve many problems associated with the delivery of different novel drugs through different delivery routes.
A Convenient One-Pot Synthesis of Aralkyl Bromides and Iodides by Reductive Halogenation of Aromatic Carbonyl Compounds (1988)

Aromatic aldehydes, ketones, carboxylic acids, and esters are converted in high yields to the corresponding aralkyl bromides or iodides by a one-pot procedure which consists of quenching the complex formed from lithium aluminium hydride and the starting material with hydrogen bromide or iodide.
Actin cable dynamics in budding yeast (2002)

Actin cables, bundles of actin filaments that align along the long axis of budding yeast, are crucial for establishment of cell polarity. We fused green fluorescent protein (GFP) to actin binding protein 140 (Abp140p) and visualized actin cable dynamics in living yeast. We detected two populations of actin cables: (i) bud-associated cables, which extend from the bud along the mother-bud axis, and (ii) randomly oriented cables, which are relatively short. Time-lapse imaging of Abp140p-GFP revealed an apparent increase in the length of bud-associated actin cables. Analysis of movement of Abp140p-GFP fiduciary marks on bud-associated cables and fluorescence loss in photobleaching experiments revealed that this apparent elongation occurs by assembly of new material at the end of the cable within the bud and movement of the opposite end of the cable toward the tip of the mother cell distal to the bud. The rate of extension of the tip of an elongating actin cable is 0.29 +/- 0.08 microm/s. Latrunculin A (Lat-A) treatment completely blocked this process. We also observed movement of randomly oriented cables around the cortex of cells at a rate of 0.59 +/- 0.14 microm/s. Mild treatment with Lat-A did not affect the velocity of movement of randomly oriented cables. However, Lat-A treatment did increase the number of randomly oriented, motile cables per cell. Our observations suggest that establishment of bud-associated actin cables during the cell cycle is accomplished not by realignment of existing cables but by assembly of new cables within the bud or bud neck, followed by elongation.
Thermoregulation of protein synthesis in Borrelia burgdorferi (1990)

Borrelia burgdorferi, the etiological agent of Lyme disease, infects humans via the bite of a tick. The microbe survives in at least two vastly different environments: an arthropod vector and a warm-blooded host. We examined protein synthesis in B. burgdorferi B31 in response to sudden heat stress, which is similar to that which occurs during the transmission from vector to host. Proteins synthesized after shifts from 28 degrees C to higher temperatures and in pulse-chase experiments were labeled with 3H-labeled amino acids for 4 h and characterized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and fluorography. The synthesis of four proteins we designated as heat stress proteins (HSPs) was increased by shifts to higher temperatures (HSP-1, 75 kilodaltons [kDa]; HSP-2, 42 kDa; HSP-3, 39 kDa; and HSP-4, 27 kDa); and the amount of one protein we designated as heat-labile protein 1 (29.5 kDa) was decreased at higher temperatures. At 37 to 40 degrees C, the major heat stress protein, HSP-1, represented 14 to 18% of the total cell protein compared with 1 to 2% of the total cell protein at 28 degrees C. HSP-1 was stable during a 4-h chase at either 40 or 28 degrees C. Demonstration of similar HSPs in low-passage, pathogenic strains of B. burgdorferi suggests that the heat stress response may be common among B. burgdorferi strains and may play a role in Lyme disease.