Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence requirements for transcriptional arrest in exon 1 of the human adenosine deaminase gene

We have previously demonstrated that a transcriptional arrest site exists in exon 1 of the human adenosine deaminase (ADA) gene and that this site may play a role in ADA gene expression (Z. Chen, M. L. Harless, D. A. Wright, and R. E. Kellems, Mol. Cell. Biol. 10:4555-4564, 1990). Sequences involved in this process are not known precisely. To further define the template requirements for transcriptional arrest within exon 1 of the human ADA gene, various ADA templates were constructed and their abilities to confer transcriptional arrest were determined following injection into Xenopus oocytes. The exon 1 transcriptional arrest signal functioned downstream of several RNA polymerase II promoters and an RNA polymerase III promoter, implying that the transcriptional arrest site in exon 1 of the ADA gene is promoter independent. We identified a 43-bp DNA fragment which functions as a transcriptional arrest signal. Additional studies showed that the transcriptional arrest site functioned only in the naturally occurring orientation. Therefore, we have identified a 43-bp DNA fragment which functions as a transcriptional arrest signal in an orientation-dependent and promoter-independent manner. On the basis of our findings, we hypothesize that tissue-specific expression of the ADA gene is governed by factors that function as antiterminators to promote transcriptional readthrough of the exon 1 transcriptional arrest site.
Micturition in rats: a chronic model for study of bladder function and effect of anesthetics.

The volume-evoked micturition reflex (VEMR) and the effects of anesthetics on the VEMR were studied in a chronic unanesthetized rat model. The bladder catheter was implanted chronically through a laparotomy and externalized percutaneously. An intrathecal (IT) catheter was implanted chronically in animals scheduled for an IT injection. By 2 days after implantation, infusion of saline (200 microliter/min) in the bladder reliably resulted in a low base-line pressure (BP) followed by a transient increase in bladder pressure, an opening of the sphincter (bladder opening pressure, BOP) corresponding to expression of urine (volume of urination, V), then a further rise in pressure (peak pressure, PP) and a subsequent return to base line. Seven days after implantation, values (means +/- SE) for BP, BOP, PP, and V were 10 +/- 0.3, 30 +/- 2, 67 +/- 6 cmH2O, and 1.0 +/- 0.1 ml, respectively. Residual volumes were reliably less than 2-4% of the expressed volume. The VEMR was reliably evoked up to 28 days after implantation. V values in unimplanted and implanted animals were not different. In implanted animals, VEMR parameters were not different during infusion or during spontaneous urination after oral fluid load. Administration of pentobarbital sodium (50 mg/kg ip), alpha-chloralose (130 mg/kg ip), ketamine (100 mg/kg im), halothane (in air 2%), and local anesthetics (2-chloroprocaine 3% or bupivacaine 0.75%, 10 microliter IT) produced a complete blockade of the VEMR and overflow incontinence at pressures significantly higher than BOP values. To compare overflow pressures and passive compliance of the bladder, unanesthetized animals were decapitated. (ABSTRACT TRUNCATED AT 250 WORDS)
Respiratory and enzymatic properties of squid heart mitochondria.

Mitochondria isolated from systemic hearts of the squid Illex illecebrosus showed high respiratory control ratios, and, with appropriate substrates, the expected ADP/O ratios. Of amino acids tested, proline and ornithine were oxidized at highest rates; of carboxylates, malate, succinate and pyruvate gave the highest state-3 respiration rates. Pyruvate oxidation is enhanced with proline, ornithine, and 1-pyrroline-5-carboxylate (pyrroline carboxylate) all of which can serve to augment the Krebs cycle. However, proline, ornithine and pyrroline carboxylate oxidation is not similarly dependent upon pyruvate. Rotenone inhibited state-3 respiration of malate, proline, ornithine and pyrroline carboxylate. Neither intermediates of fatty acid oxidation nor glycerol 3-phosphate were utilized at significant rates. Key enzymes in proline and ornithine oxidation, i.e. proline dehydrogenase, pyrroline-carboxylate dehydrogenase, ornithine aminotransferase, and glutamate dehydrogenase were located in the mitochondria. The synthesis of proline is catalyzed by pyrroline-carboxylate reductase, which was found exclusively in the cytosol. The respiration, phosphorylation and enzyme data taken together suggest that the main carbon sources for heart mitochondria of Illex are pyruvate plus the proline and ornithine pool.
Effects of duloxetine, an antidepressant drug candidate, on concentrations of monoamines and their metabolites in rats and mice.

Duloxetine, (+)-N-methyl-3-(1-naphthalenyloxy)-2-thiophenepropanamine, is an inhibitor of the serotonin and norepinephrine neuronal transporters (Wong et al., 1993). In mice, duloxetine antagonized the depletion of brain serotonin by p-chloroamphetamine (ED50 = 2.5 mg/kg, i.p.) and the depletion of heart norepinephrine by 6-hydroxydopamine (ED50 = 1.1 mg/kg, i.p.). Brain concentrations of 5-hydroxyindoleacetic acid were decreased by duloxetine at 2 hr after doses of 1, 3 and 10 mg/kg and at 1 to 8 hr (but not 24 hr) after a 10 mg/kg i.p. dose of duloxetine. Duloxetine antagonized norepinephrine depletion in frontal cortex, but not dopamine depletion in striatum, after treatment of mice with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine. In rats, duloxetine decreased brain 5-hydroxyindoleacetic acid dose-dependently for up to 8 hr and decreased serotonin turnover measured by the accumulation of 5-hydroxytryptophan in rat hypothalamus after decarboxylase inhibition. In rats, duloxetine antagonized the depletion of brain serotonin by p-chloramphetamine and the depletion of norepinephrine and epinephrine in hypothalamus after i.c. v. injection of 6-hydroxydopamine. In vitro, duloxetine had little effect on either type A (serotonin as substrate) or type B (phenylethylamine as substrate) monoamine oxidase, IC50 concentrations being above 10(-5) M. These data extend evidence that duloxetine inhibits serotonin and norepinephrine transporters in vivo, actions that may lead to therapeutic efficacy in mental depression.
Evolution of diabetic nephropathy in kidney grafts. Evidence that a simultaneously transplanted pancreas exerts a protective effect.

Thirty-six renal transplant biopsies were obtained from 20 diabetic patients 1-6.5 years after successful combined pancreatic and renal transplantation (PKtx). An additional 36 renal transplant biopsies were obtained from 30 diabetic recipients 1-6.8 years after kidney transplantation only (Ktx). Light microscopic lesions indicating diabetic nephropathy were evaluated by a semiquantitative score ranging from 0 to 9. Within 2.5 years after transplantation, light microscopy showed no or only slight diabetic changes in both groups (nephropathy score = 0-2). Later, a nephropathy score > or = 3 was seen in only 1 of 15 biopsies (6.7%) in the combined PKtx group, but in 11 of 24 biopsies (45.8%) in the Ktx group (P < 0.05). Twenty-eight of the biopsies from the PKtx group and 26 of them from the Ktx patients were examined with electron microscopic morphometry to evaluate the glomerular basement membrane thickness (BMT) and the relative volume of the mesangial tissue (Vv). Of the biopsies taken < 2 1/2 years after transplantation in PKtx patients, and of those similarly taken in the Ktx patients, 93.8% vs. 88.9% had BMT values within 2 SD of the normal (NS). Of the kidney biopsies taken > or = 2.5 years after transplantation, 91.7% in the PKtx group still had a normal BMT, while only 35.3% of the biopsies in the Ktx group had a normal BMT (P < 0.01). In the PKtx group, the Vv was normal in 12/16 (75.0%) of the biopsies taken < 2 1/2 years after transplantation, and in 9/11 (81.8%) of the biopsies obtained > or = 2.5 years after transplantation. In contrast, the Vv was normal in only 1/9 (11.1%) and 2/17 (11.8%) of correspondingly obtained biopsies from Ktx patients (biopsies < 2.5 years after transplantation, P < 0.01, and biopsies > or = 2.5 years after transplantation, P < 0.001, respectively). We conclude that a functioning pancreatic transplant can prevent or reduce the various signs of diabetic nephropathy that eventually develop in diabetic patients with a kidney graft only.
Cytogenetics of lymphomas

Summary Cytogenetic analysis is now a routine part of the diagnosis and management of a significant number of lymphoid malignancies. Whilst conventional cytogenetics remains the most comprehensive method for assessing chromosome abnormalities, the technical difficulties associated with conventional cytogenetics in most lymphomas has resulted in increased use of fluorescence in situ hybridisation (FISH) to identify specific abnormalities that are useful in either the diagnosis or management of these disorders. The finding of one of the Burkitt's translocations is of major importance in the diagnosis of Burkitt's and Burkitt's‐like lymphomas, whereas the t(14;18), although seen in most follicular lymphomas (FL), is not usually required to make a diagnosis. Thus, whilst cytogenetics may be of interest in FL, it is not an essential part of the diagnostic work‐up. Conventional cytogenetics may be useful for identifying markers of resistance to Helicobacter pylori therapy in MALT lymphomas. In disorders such as Hodgkin lymphoma, hairy cell leukaemia and lymphoplasmacytoid lymphoma, although many cytogenetic abnormalities have been observed, no consistent or specific abnormalities have been identified and so, at this point in our knowledge of the genetics of these disorders, cytogenetics cannot be considered a useful test for either diagnosis or prognosis. In contrast, the diagnosis of mantle cell lymphoma is now dependent upon the identification of the 11;14 translocation that results in cyclin D1 up‐regulation. It is widely acknowledged that FISH is the most consistently useful test to identify the juxtaposition of the CCND1 and IGH genes in mantle cell lymphoma and is regarded as the ‘gold standard’. FISH also has a role in identifying genetic abnormalities of prognostic significance in chronic lymphocytic leukaemia. Given the wealth of genetic and cytogenetic abnormalities that are continuing to be found in chronic lymphoid malignancies, it will be some time before the optimal use of both conventional cytogenetics and FISH is established in the diagnosis and management of lymphomas.Abbreviations: BL, Burkitt's lymphoma; BLL, Burkitt's‐like lymphoma; CGH, comparative genomic hybridisation; CLL, chronic lymphocytic leukaemia; DLBCL, diffuse large B‐cell lymphoma; FISH, fluorescence in situ hybridisation; FL, follicular lymphoma; HL, Hodgkin lymphoma M‐FISH; multicolour FISH; MALT, mucosa‐associated lymphoid tissue; MCL, mantle cell lymphoma; MZBCL, marginal zone B‐cell lymphoma; NHL, non‐Hodgkin lymphoma; SKY, spectral karyotyping.
Operative Management of Lower Extremity Fractures in Patients With Head Injuries

Treatment of patients with lower extremity fractures and concomitant head injury is controversial. The authors compared reamed intramedullary nailing versus plating of femoral and tibial fractures in patients with polytrauma and concomitant head injury. One thousand five hundred twenty-five patients with head injuries were identified from a prospective trauma database. Of those, 1211 patients sustained severe head injuries (Abbreviated Injury Score ≥ 3). One hundred nineteen patients with severe head injuries and lower extremity long bone fractures met the inclusion criteria. Ultimately, four patient groups were identified: Group A, reamed femoral nail (n = 21); Group B, femoral plate (n = 29); Group C, reamed tibial nail (n = 23); and Group D, tibial plate (n = 46). Reamed intramedullary nails did not significantly alter the risk of mortality when compared with plates in femoral (relative risk 0.46; 95% confidence interval, 0.04–4.6) and tibial (relative risk 1.18; 95% confidence interval, 0.05–11.9) fractures. The severity of the initial head injury (Glasgow Coma Scale score) was the strongest predictor of mortality. Functional independence scores between patients with reamed nails and patients with plates were similar at 1 year. Head injury does not seem to be a contraindication to reamed intramedullary nailing in patients with lower extremity fractures. The severity of head injury alone is an important predictor of outcome. A large, randomized trial with sufficient study power is needed to clarify this issue.
Dynamic Cardiophysiologic Variables Correlate with Lesion Location and FIMTM in Patients with Ischemic Stroke

Arad M, Ring H, Abboud S, Radai MM, Tamir A, Adunsky A: Dynamic cardiophysiologic variables correlate with lesion location and FIMTM in patients with ischemic stroke. Am J Phys Med Rehabil 2002;81:590–596. Objective To examine the correlation between a clinical measure of function in patients undergoing rehabilitation who had recently had an ischemic stroke and to examine cardiophysiologic measures registered during effort. Design A cohort study comprising a sample of consecutive patients, without a history of cardiac disease or rhythm disturbances, admitted for rehabilitation after an ischemic supratentorial stroke. All patients were examined for the FIM™ score and dynamic cardiophysiologic variables. Results were analyzed in relation to stroke location. Thirty-eight patients participated in the study. Ten patients had a superficial lesion, 20 had a deep brain lesion, and eight had no noticeable lesion by computed tomographic imaging. Function was measured with the FIM instrument 48–72 hr after admission and repeated at 1 wk before discharge. Electrocardiographic activity was recorded during physiotherapy treatment. The relationship between the RR and QT intervals in the electrocardiographic waveforms was found to estimate two cardiophysiologic variables, the constant (a) and the slope (b) values, reflecting the dynamic change of QT during physiotherapy effort. Results Only for the subgroup of patients who sustained a deep brain lesion did the motor items in the FIM instrument on admission and discharge scores have a statistically significant relationship with the slope variable (b) and an inverse statistically significant relationship with the constant variable (a). Conclusions Deep brain infarction seems to result in a significant dysfunction of the autonomic nervous system, manifesting itself as distorted dynamic behavior of the QT interval and with impaired functional performance.
Changes in aphid probing behaviour as a function of insect age and plant resistance level

Abstract Aphids perform a series of behaviours to assess feeding suitability and, hence, to select a plant. Little information, however, is available on such behaviour after aphids have settled on a plant. Observation of probing behaviour over an extended period of time can improve our understanding of insect-plant interactions and is instrumental in the study of crop resistance. Here, we assessed the influence of aphid age and plant resistance level on aphid behaviour. An electrical penetration graph (EPG) technique was implemented to monitor the behaviour of potato aphid, Macrosiphum euphorbiae, alates on potato, Solanum tuberosum, and on both a susceptible and a resistant genotype of a wild Solanum species, S. chomatophilum. The behaviour was measured at daily intervals for the first seven days following adult emergence. The results indicated independent and interacting effects of aphid age and plant genotype on probing behaviour. Some behavioural discrepancies between susceptible and resistant genotypes were only observed after the first day, thus highlighting the limits of punctual one-day behavioural studies to assess plant resistance mechanisms. Our work supports the hypothesis that aphids continuously adapt their behaviour to the plant characteristics.
Neutrophils Rolling on Immobilised Platelets Migrate into Homotypic Aggregates after Activation

Summary Interactions between platelets and leucocytes are implicated in the pathology of thrombotic vascular disease. Using a flow-based adhesion assay we have investigated a novel route for the formation of neutrophil aggregates on the surface of immobilised activated platelets. Neutrophils perfused over a platelet monolayer formed numerous rolling attachments but rapidly stopped and spread after the superfusion of N-formyl-methionyl-leucyl-phenylalanine or platelet-activating factor (both at 10–7 M). Subsequent integrin-mediated migration across the platelet monolayer enabled formation of homotypic neutrophil aggregates, which was significant within 2.5 min of receipt of either stimulus. Aggregates increased in size with time and had an average projected area of ~500 μm2 after 10 min. Increasing size was correlated with an increasing tendency for movement downstream and large aggregates sometimes tumbled in that direction. The formation and stability of homotypic aggregates was dependent on several adhesive mechanisms. Antibody blockade demonstrated that interactions involving CD11a/ CD18 and ICAM-3, between αvβ3-integrin and CD31 and between L-selectin and an unidentified counter-ligand were all required for the complete aggregatory response. Furthermore, blockade of L-selectin allowed initial aggregation which then reversed, suggesting that this receptor might regulate the interactions between other adhesion molecules that directly supported cell-cell adhesion. We propose that this novel route for leucocyte aggregation could promote vascular occlusion in thrombotic vessels or at distal sites in the event of embolisation.
Antibodies purified from sera of HIV-1-infected patients by affinity on the heptad repeat region 1/heptad repeat region 2 complex of gp41 neutralize HIV-1 primary isolates

Objective:The objective of this paper was to evaluate the presence and the neutralizing activity of antibodies directed against the complex formed between the two heptad repeat regions (HR1 and HR2) of HIV-1 gp41 in sera of HIV-1-infected patients. Research designs and methods:The HR1 region was represented by the peptide N36 and the maltose-binding protein (MBP)–HR1, the HR2 region by the peptide C34 and MBP44. Antibodies directed to the HR1/HR2 complex were purified from sera by affinity chromatography using MBP–HR1/C34 adsorbed onto a resin. Results:First, we demonstrated that human monoclonal antibodies, which are directed specifically to the HR1/HR2 complex recognized in enzyme-linked immunosorbent assay the MBP–HR1/C34 and MBP44/N36 mixtures but not the proteins or the peptides individually. We investigated the ability of 50 sera of HIV-1-infected patients to react with the MBP–HR1/C34 and MBP44/N36 complexes. We found that the majority of sera of HIV-1-infected patients recognized the HR1/HR2 complexes but not or to a lower extent the proteins or the peptides individually. Antibodies purified from sera by affinity chromatography using MBP–HR1/C34 adsorbed to a resin neutralized different primary HIV-1 isolates. Conclusion:The presence of antibodies directed to the HR1/HR2 complex in sera of HIV-infected patients highlights the immunogenic character of the complex, whereas the neutralizing activity of these antibodies suggests that immunogens representing HIV-1 HR1/HR2 complexes might be used in anti-HIV vaccine.
Structural and Biochemical Characterization of Plasmodium falciparum 12 (Pf12) Reveals a Unique Interdomain Organization and the Potential for an Antiparallel Arrangement with Pf41*

Background: Pf12 is the archetypal member of the 6-Cys protein family, members of which are important Plasmodium vaccine targets. Results: Purifying selection and apical localization of Pf12, crystal structure of tandem 6-Cys domains, and mass spectrometry of cross-linked Pf12-Pf41 heterodimer are shown. Conclusion: A functionally important role for Pf12 and potential for antiparallel heterodimer is provided. Significance: First full-length 6-Cys protein structure and first details of heterodimer organization are revealed. Plasmodium falciparum is the most devastating agent of human malaria. A major contributor to its virulence is a complex lifecycle with multiple parasite forms, each presenting a different repertoire of surface antigens. Importantly, members of the 6-Cys s48/45 family of proteins are found on the surface of P. falciparum in every stage, and several of these antigens have been investigated as vaccine targets. Pf12 is the archetypal member of the 6-Cys protein family, containing just two s48/45 domains, whereas other members have up to 14 of these domains. Pf12 is strongly recognized by immune sera from naturally infected patients. Here we show that Pf12 is highly conserved and under purifying selection. Immunofluorescence data reveals a punctate staining pattern with an apical organization in late schizonts. Together, these data are consistent with an important functional role for Pf12 in parasite-host cell attachment or invasion. To infer the structural and functional diversity between Pf12 and the other 11 6-Cys domain proteins, we solved the 1.90 Å resolution crystal structure of the Pf12 ectodomain. Structural analysis reveals a unique organization between the membrane proximal and membrane distal domains and clear homology with the SRS-domain containing proteins of Toxoplasma gondii. Cross-linking and mass spectrometry confirm the previously identified Pf12-Pf41 heterodimeric complex, and analysis of individual cross-links supports an unexpected antiparallel organization. Collectively, the localization and structure of Pf12 and details of its interaction with Pf41 reveal important insight into the structural and functional properties of this archetypal member of the 6-Cys protein family.