gebhart/patrepeval huggingface dataset:
Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum (2017)

Gene expression in Plasmodium falciparum is tightly regulated to ensure successful propagation of the parasite throughout its complex life cycle. The earliest transcriptomics studies in P. falciparum suggested a cascade of transcriptional activity over the course of the 48-hour intraerythrocytic developmental cycle (IDC); however, the just-in-time transcriptional model has recently been challenged by findings that show the importance of post-transcriptional regulation. To further explore the role of transcriptional regulation, we performed the first genome-wide nascent RNA profiling in P. falciparum. Our findings indicate that the majority of genes are transcribed simultaneously during the trophozoite stage of the IDC and that only a small subset of genes is subject to differential transcriptional timing. RNA polymerase II is engaged with promoter regions prior to this transcriptional burst, suggesting that Pol II pausing plays a dominant role in gene regulation. In addition, we found that the overall transcriptional program during gametocyte differentiation is surprisingly similar to the IDC, with the exception of relatively small subsets of genes. Results from this study suggest that further characterization of the molecular players that regulate stage-specific gene expression and Pol II pausing will contribute to our continuous search for novel antimalarial drug targets.
Short Allele of 5‐HTTLPR as a Risk Factor for the Development of Psychosis in Japanese Methamphetamine Abusers (2008)

Accumulating evidence suggests that genetic factors contribute to the vulnerability to methamphetamine (MAP) abuse and associated psychiatric symptoms. Chronic MAP abuse leads to psychosis, which may be of a transient or a prolonged type. Serotonergic dysfunction has been proposed as one of the contributory factors in the development of MAP psychosis. Our PET studies revealed that the serotonin transporter (5-HTT) density in global brain regions is significantly lower in MAP abusers. In this study, we examined the role of a functional polymorphism in the 5' flanking region of the 5-HTT gene (5-HTTLPR) in the development of MAP psychosis in a Japanese population. We analyzed DNA samples from 166 MAP patients (95 with transient and 71 with prolonged psychosis) and 197 age-, sex-, and geographic-origin-matched healthy controls. Patients were also subdivided according to the presence (n= 119) or absence (n= 148) of spontaneous relapse. We observed significant genotypic association of the 5-HTTLPR polymorphism with MAP psychosis (P= 0.022), particularly in patients who show prolonged psychosis. The frequency of the S allele in patients with prolonged psychosis was significantly higher than that of the controls (P= 0.045); it was further higher in patients with prolonged psychosis with spontaneous relapse (P= 0.004). 5-HTTLPR has been suggested to regulate the transcriptional activity of 5-HTT, with S alleles showing lesser transcriptional efficiency and also lower 5-HT(1A) receptor-binding potential. Prolonged MAP use, combined with the high frequency of 5-HTTLPR S-alleles, may lead to reduced 5-HTT levels and 5-HT(1A) receptor-binding potential in the brain, resulting in the dysfunction of the serotonergic system. Thus, we suggest a possible role for the 5-HTTLPR polymorphism in MAP psychosis.
ChemInform Abstract: Reactions of 3‐Amino‐Substituted 5,6‐Dihydro‐2H‐1,4‐oxazines with α‐Halo Ketones. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Throughput enhancement of IEEE 802.11 WLAN via frame aggregation (2005)

The popular IEEE 802.11 WLAN is known to achieve relatively small throughput performance compared to the underlying physical layer (PHY) transmission rate. This is due mainly to the large overheads composed of medium access control (MAC) header, PHY preamble/header, backoff time, acknowledgement (ACK) transmission, and some inter-frame spaces (IFSs). Since these overheads are added to each frame transmission, the throughput degradation is relatively high with small-size frames. In this paper, we present a frame aggregation (FA) scheme, which can improve the throughput performance. By aggregating small-size frames into a large frame, we can reduce these overheads relatively. We propose a simple method to implement the FA into the real testbed using off-the-shelf products via device driver modifications. The performance of the FA is evaluated by both numerical analysis and actual measurements from the real testbed. According to the measurement results, the FA can improve the throughput performance by 2 to 3 Mbps, when multiple frames are aggregated.
Effect of Pretransplant Serum Creatinine on the Survival Benefit of Liver Transplantation (2009)

More candidates with creatinine levels >or= 2 mg/dL have undergone liver transplantation (LT) since the implementation of Model for End-Stage Liver Disease (MELD)-based allocation. These candidates have higher posttransplant mortality. This study examined the effect of serum creatinine on survival benefit among candidates undergoing LT. Scientific Registry of Transplant Recipients data were analyzed for adult LT candidates listed between September 2001 and December 2006 (n = 38,899). The effect of serum creatinine on survival benefit (contrast between waitlist and post-LT mortality rates) was assessed by sequential stratification, an extension of Cox regression. At the same MELD score, serum creatinine was inversely associated with survival benefit within certain defined MELD categories. The survival benefit significantly decreased as creatinine increased for candidates with MELD scores of 15 to 17 or 24 to 40 at LT (MELD scores of 15-17, P < 0.0001; MELD scores of 24-40, P = 0.04). Renal replacement therapy at LT was also associated with significantly decreased LT benefit for patients with MELD scores of 21 to 23 (P = 0.04) or 24 to 26 (P = 0.01). In conclusion, serum creatinine at LT significantly affects survival benefit for patients with MELD scores of 15 to 17 or 24 to 40. Given the same MELD score, patients with higher creatinine levels receive less benefit on average, and the relative ranking of a large number of wait-listed candidates with MELD scores of 15 to 17 or 24 to 40 would be markedly affected if these findings were incorporated into the allocation policy.
Correction: Dynamic Scaling in the Growth of a Non-Branching Plant, Cardiocrinum cordatum (2012)

We investigated whole-plant leaf area in relation to ontogenetic variation in leaf-size for a forest perennial herb, Cardiocrinum cordatum. The 200-fold ontogenetic variability in C. cordatum leaf area followed a power-law dependence on total leaf number, a measure of developmental stage. When we normalized for plant size, the function describing the size of single leaves along the stem was similar among different-sized plants, implying that the different-sized canopies observed at different times in the growth trajectory were fundamentally similar to each other. We conclude that the growth trajectory of a population of C. cordatum plant leaves obeyed a dynamic scaling law, the first reported for a growth trajectory at the whole-plant level.
Transparent dissemination of adapters in Jini (2002)

Jini is a Java-based technology for 'spontaneous' distributed computing which enables programs to dynamically discover nearby services by means of a type-based lookup mechanism. However, this mechanism requires that all the parties involved first agree on a set of common wellknown interfaces for describing services which offer the same high-level functionalities. We believe that this mechanism will in some situations prove to be too rigid or complex and that "interface fragmentation" will inevitably happen. We propose a mechanism for automatically disseminating adapters, small downloadable components that convert between types that describe similar services but are yet incompatible. The implementation of the solution consists in the definition of a new Jini service, the Adapter Service, which is a repository for adapters that registers adapter-augmented proxy objects with the Jini Lookup Service when new services appear on the network. This solution does not require any modification to clients, services or to the Lookup Service.
CAMEL NANOBODIES NEUTRALIZE SARS-COV-2 VARIANTS (2023)

Abstract Background and Significance With the emergence of SARS-CoV-2 variants during the global pandemic from 2020 to 2023, there is need for broadly neutralizing antibodies. Due to their small size and unique conformations, nanobodies can recognize protein cavities that are not accessible to conventional antibodies. Methods and Results Here, we used phage display libraries built from dromedary camels to isolate two VHH nanobodies (7A3 and 8A2), which have high affinity for the receptor-binding domain (RBD) of the SARS-CoV-2 spike. Cryo-EM complex structures revealed that 8A2 binds the RBD in its up mode and 7A3 targets a conserved and deeply buried site in the spike regardless of the conformational state of the RBD. At a dose of ≥5 mg/kg, nanobody 7A3 efficiently protected K18-hACE2 transgenic mice from the lethal challenge of SARS-CoV-2 variants B.1.351 or B.1.617. With the addition of omicron variant, a new VHH nanobody (J1B4) was isolated to target the S2 subunit of the SARS-CoV-2 spike that can bind across many variants including omicron. Trispecific nanobodies were made using 7A3, 8A2, and J1B4 which had increased binding signals compared to the nanobodies alone. Using this method, we hope to create a therapeutic that is able to broadly neutralize not only all pre-existing variants of SARS-CoV-2, but also be effective towards future SARS-CoV related variants. Conclusions and Future Directions By combining nanobodies targeting the RBD of the S1 subunit (7A3+8A2) with a nanobody targeting the S2 subunit (J1B4), we can increase the chance of protection against all SARS-CoV-2 infections. Due to the increased protein binding of the trispecific compared to individual nanobodies alone, it shows great promise that the trispecific may be able to enhance its activity across all variants. Nanobody-based therapeutics may be developed as a nasal spray which can be self-administered and inhaled directly to the lungs to treat the infection at its source.
The Effect of Ring Size on Catenane Synthesis (2003)

Abstract The synthesis of a [2]catenane with 87‐membered rings was improved and extended to [2]catenanes with 63‐ and 147‐membered rings. One of the key features is the carbonate linkage between phenols with tolane substituents in the 2‐ and 6‐positions, which serves as a covalent template for the geometrical arrangement of a macrocycle and a ring precursor. Subsequent cyclization of the threaded ring precursor gives the precatenane as the main product, and this is converted into the catenane by carbonate hydrolysis. As well as the precatenane, its dumbbell shaped isomer is formed in the cyclization step. From the known conformation of the templating carbonate moiety and the strong dependence of the ratio of precatenane and dumbbell on the ring size, the dumbbell's origin is attributed to the conformational flexibility of the large rings and not to geometrical ambiguity of the carbonate moiety. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2003)
Body-voltage estimation in digital PD-SOI circuits and its application to static timing analysis (2001)

Partially depleted silicon-on-insulator (PD-SOI) has emerged as a technology of choice for high-performance low-power deep-submicrometer digital integrated circuits. An important challenge to the successful use of this technology involves successfully managing and predicting the large "uncertainties" in the body potential and consequently the threshold voltages that can result from unknown past switching activity. In this paper, we present a unique state-diagram abstraction of the PD-SOI field-effect transistor that can capture all of the past switching activity determining the body voltage. Based on this picture, four different estimation schemes are discussed that increasingly bound floating body uncertainty based on more detailed knowledge of switching activity. Using these estimation techniques within a prototype transistor-level static timing analysis engine, we demonstrate both the accuracy of the estimation and the reduction in delay uncertainty possible with these techniques.
Comprehensive lipid profiling of early stage oocytes and embryos by MRM profiling (2018)

Figure S1: (A) 2D PCA Score Plot for bovine oocytes (IO and OM). (B) Volcano plot showing lipids (pink dots identified by a numeric code) that presented FC > 1.5 and p < 0.05 in the comparison of IO vs. OM. The list of specific lipids is shown in table S2. Figure S2: (A) 2D PCA Score Plot for bovine gametes (OM and 2C for mature oocytes and 2-cell embryos, respectively). (B) Volcano plot showing lipids (pink dots identified by a numeric code) that presented FC > 2 and p < 0.05 in the comparison 2C vs. OM. Differential lipids are listed by class at Table 2 and individually at Table S3. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Immunocytochemical study of the interaction of soybean trypsin inhibitor with rat intestinal mucosa. (1978)

To investigate further the cause of the pancreatic enlargment induced by orally ingested soybean trypsin inhibitor (STI), antibodies raised against STI and purified by affinity chromatography were used to localise dietary STI in the rat gut by fluorescent immunocytochemical methods. This technique permitted the clear intracellular demonstration of STI in the ileal mucosa of suckling rats. However, in adult rats no entry of STI into mucosal cells of the small intestine could be demonstrated, it being confined to the luminal surface of the mucosa. Although the passage of STI into and across the adult intestinal mucosa could not be excluded through the use of this technique, the results are consistent with an intraluminal mode of action of STI as suggested by Green and Lyman (1972)--namely, that the pancreatic enlargement caused in sensitive species results from the inhibition of trypsin (which acts as the physiological inhibitor of the mucosal secretion of pancreotrophic hormones), thus resulting in the uninhibited secretion of these hormones.
Injection schemes for TWT linearization (2003)

Summary form only given, as follows. Summary form only given. Traveling Wave Tubes (TWTs), widely used as microwave amplifiers for communication applications due to their high power outputs, are desired to have high linearity and efficiency. The nonlinear behavior of these tubes leads to significant intermodulation and harmonic distortion in the output spectrum. A scheme based on amplitude and phase optimized second-harmonic injection to suppress nonlinear products in a TWT, has been proposed and studied both experimentally and analytically. Equalizers that effectively employ IM3 (third-order intermod) injection have been used to balance the nonlinear AM/AM (amplitude distortion) and AM/PM (phase distortion) effects. We are performing a detailed investigation of the harmonic and IM3 injection schemes, both experimentally and by simulations. Experimental studies have shown comparable IM3 suppression of /spl sim/30dB for both schemes, at the same time providing some insights into why harmonic injection might be preferable. Another scheme utilizing simultaneous harmonic and IM3 injection has been conceptually demonstrated, that has the prospect of eliminating the phase sensitivity of the two latter schemes. Simulations using the frequency domain, large-signal TWT code, LATTE are being carried out to interpret the experimental observations and device physics.
Martine CHARAGEAT, La Délinquance matrimoniale. Couples en conflit et justice en Aragon (XVe-XVIe s.) (2011)

L’ouvrage de Martine Charageat montre le regain d’intérêt des historiens pour la cellule conjugale et pour les archives judiciaires. C’est un livre important parce qu’il adopte une véritable démarche de genre. L’auteure étudie les couples aragonais du début du xve siècle au concile de Trente par le biais des conflits matrimoniaux révélés par des actes de la procédure provenant de quatre juridictions (le tribunal de l’officialité de Saragosse et les tribunaux séculiers des juges urbains de Sar...
Intelligent warning sign system utilising printed functionalities and hybrid integration (2014)

The direct medical care cost of all hospital treated injuries in the EU is estimated to be at least 78 billion Euros each year. Therefore, significant savings can be achieved in economical and human resources, when amount of injuries are decreased. Intelligent and active warning sign can prevent accidents more effectively than traditional passive graphical warning sign. Intelligent and active warning sign alerts person approaching potentially dangerous spot using both visual and audible warning. In areas without infrastructure, however, intelligent warning sign need to be autonomous. We have manufactured an intelligent and autonomous warning sign prototype utilising printed functionalities and hybrid integration. Our intelligent warning sign system utilises low energy radio network operating at 2.4 GHz ISM waveband in wireless communication. Radio system provides wireless link to other warning signs nearby and up and down gateway to server. In addition, system retains energy harvesting system based on flexible solar cell and bendable Li-Ion battery. Sensing is based on infrared sensor enabling person detection by emitted thermal radiation from 2 meter distance. Microcontroller decodes sensor signal and controls operations for warning signals based on six blinking LEDs and beeping buzzer. LED flexible substrate was PET foil on which conductive traces were printed using Asahi 411AW silver ink. Miniature high brightness 0402 size μSMD LEDs producing up to 50 mcd in ±65° angle were bonded on PET foil using isotropic conductive adhesive, type EPOTEK H20E. Final measures of the prototype were 75 mm × 220 mm with maximum thickness of 20 mm and weight of 58 grams. System assembly with rigid central part and flexible flanges enabled prototype attachment on flat, angulated or curved surfaces. Implemented warning sign system platform offers also possibility to implement other intelligent guiding and sensing information transmission applications in areas lacking connection to grid and wired Internet.
Cloning and Functional Expression of a Soluble Form of Kynurenine/α -Aminoadipate Aminotransferase from Rat Kidney (1995)

Several aminotransferases with kynurenine aminotransferase (KAT) activity are able to convert L-kynurenine into kynurenic acid, a putative endogenous modulator of glutamatergic neurotransmission. In the rat, one of the described KAT isoforms has been found to correspond to glutamine transaminase K. In addition, rat kidney alpha-aminoadipate aminotransferase (AadAT) also shows KAT activity. In this report, we describe the isolation of a cDNA clone encoding the soluble form of this aminotransferase isoenzyme from rat (KAT/AadAT). Degenerate oligonucleotides were designed from the amino acid sequences of rat kidney KAT/AadAT tryptic peptides for use as primers for reverse transcription-polymerase chain reaction of rat kidney RNA. The resulting polymerase chain reaction fragment was used to screen a rat kidney cDNA library and to isolate a cDNA clone encoding KAT/AadAT. Analysis of the combined DNA sequences indicated the presence of a single 1275-base pair open reading frame coding for a soluble protein of 425 amino acid residues. KAT/AadAT appears to be structurally homologous to aspartate aminotransferase in the pyridoxal 5'-phosphate binding domain. RNA blot analysis of rat tissues, including brain, revealed a single species of KAT/AadAT mRNA of approximately 2.1 kilobases. HEK-293 cells transfected with the KAT/AadAT cDNA exhibited both KAT and AadAT activities with enzymatic properties similar to those reported for the rat native protein.
FABRICATION OF A 3 m Ø x 5 m SUPERCONDUCTING SOLENOID FOR THE FERMILAB COLLIDER DETECTOR FACILITY (1984)

The 3mØ x 5m (1.5 Tesla) superconducting solenoid for the Fermilab Collider Detector Facility (CDF) is under construction in Japan. The coil consists of a single layer aluminum-stabilized monolithic NbTi/Cu superconductor fabricated with the EFT (extrusion with front tension) method. The forced flow cooling method of two-phase helium is used. In order to minimize the material thickness of the solenoid the coil is built without a permanent inner bobbin. The radial electromagnetic forces are supported by an aluminum cylinder placed radially outside the coil. The completed coil wounded on the removable mandrel is shrink-fitted with the support cylinder. Results of development work are presented.
Alterations in erythrocyte adenine nucleotide pools resulting from 2'-deoxycoformycin therapy. (1983)

2'-Deoxycoformycin, a tight-binding adenosine deaminase inhibitor, was administered to 11 adult patients with refractory lymphoproliferative diseases. Total doses ranged from 1.0 to 13.5 mg/kg. Inhibition of lymphoblast adenosine deaminase was obtained in all cases and tumor cytoreduction was noted in eight of ten cases, but no clinically meaningful remissions were obtained. Major toxicities occurred in five patients and included pulmonary edema, renal failure, central nervous system toxicity, hypotension, and death. Toxicity prevented retreatment in several cases in which marked cytoreduction occurred. Deoxyadenosine triphosphate accumulated to a variable extent in the red blood cells of all patients, and a reciprocal decrease in erythrocyte adenosine triphosphate was noted in all cases but one. All patients who suffered major organ toxicity had red blood cell deoxyadenosine triphosphate/adenosine triphosphate ratios greater than 1.3. These data suggest that the degree of replacement of adenosine triphosphate by deoxyadenosine triphosphate in erythrocytes reflects the biochemical milieu which may result in systemic toxicity following treatment with 2'-deoxycoformycin.
Precision X-Y robotic object handling using a dual GMR bridge sensor (2000)

A dual integrated GMR bridge sensor, which is able to simultaneously detect x and y components of an external magnetic field, was demonstrated, and applied to the precision robotic placement of objects. Two orthogonal GMR bridges are used, biased by two sets of integrated Co/sub 78/Pt/sub 22/ film permanent magnets with different coercivities (1230 Oe and 522 Oe, respectively). The field sensitivity is 0.35 mV/(V/spl times/Oe) in each field direction. For the positioning application, an absolute accuracy of 10 /spl mu/m in x-direction has been achieved over more than 1900 cycles which is insensitive to sensor offsets and thermal drifts.