Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutations That Decrease DNA Binding of the Processivity Factor of the Herpes Simplex Virus DNA Polymerase Reduce Viral Yield, Alter the Kinetics of Viral DNA Replication, and Decrease the Fidelity of DNA Replication

ABSTRACT The processivity subunit of the herpes simplex virus DNA polymerase, UL42, is essential for viral replication and possesses both Pol- and DNA-binding activities. Previous studies demonstrated that the substitution of alanine for each of four arginine residues, which reside on the positively charged surface of UL42, resulted in decreased DNA binding affinity and a decreased ability to synthesize long-chain DNA by the polymerase. In this study, the effects of each substitution on the production of viral progeny, viral DNA replication, and DNA replication fidelity were examined. Each substitution mutant was able to complement the replication of a UL42 null mutant in transient complementation assays and to support the replication of plasmid DNA containing herpes simplex virus type 1 (HSV-1) origin sequences in transient DNA replication assays. Mutant viruses containing each substitution and a lacZ insertion in a nonessential region of the genome were constructed and characterized. In single-cycle growth assays, the mutants produced significantly less progeny virus than the control virus containing wild-type UL42. Real-time PCR assays revealed that these UL42 mutants synthesized less viral DNA during the early phase of infection. Interestingly, during the late phase of infection, the mutant viruses synthesized larger amounts of viral DNA than the control virus. The frequencies of mutations of the virus-borne lacZ gene increased significantly in the substitution mutants compared to those observed for the control virus. These results demonstrate that the reduced DNA binding of UL42 is associated with significant effects on virus yields, viral DNA replication, and replication fidelity. Thus, a processivity factor can influence replication fidelity in mammalian cells.
Preparation of scaffolds from human hair proteins for tissue-engineering applications

Human hair proteins were isolated and purified for the fabrication of tissue-engineering scaffolds. Their cellular compatibility was studied using NIH3T3 mice fibroblast cells. The proteins were characterized using FTIR spectroscopy, sodium dodecyl sulfate–polyacrylamide gel electrophoresis for molecular weights and two-dimensional polyacrylamide gel electrophoresis for their isoelectric points (pIs). The molecular weights of keratins were in the range of 40–60 kilo-Daltons (kDa) and of matrix proteins were in the range of 15–30 kDa. The pIs of keratins were found to be in the range of 4.5–5.3. Sponges of the proteins were formed by lyophilization. Scanning electron microscopy was performed to examine the surface. Swelling studies were carried out in phosphate buffer saline at physiological pH 7.4. The hydrophilic character of the protein surface was studied by determining an average contact angle, which came to be 37°. The wells of tissue culture plates were coated with these proteins for studying the attachment and morphology of the cells. The protein detachment study was done to ensure the adsorption of proteins on the wells until the completion of the experiments. The cellular growth on a protein-coated surface showed three-dimensional ‘bulged’ morphology due to cell–cell and cell–matrix contacts. The sponges of human hair proteins supported more cells for a longer period than control. The morphology and cell proliferation studies exhibited by NIH3T3 cells on these proteins have shown their potential to be used as tissue-engineering scaffolds with better cell–cell contacts and leucine–aspartic acid–valine (LDV)-mediated cell–matrix interactions.
Impact of ACE Inhibitors and AII Receptor Blockers on Peritoneal Membrane Transport Characteristics in Long-Term Peritoneal Dialysis Patients

Background Long-term peritoneal dialysis (PD) may lead to peritoneal fibrosis and ultrafiltration failure. The latter occurs due to high solute transport rates and diabetiform peritoneal sclerosis. Angiotensin-II (AII) is known to be a growth factor in the development of fibrosis and a number of animal studies have shown it likely that inhibiting the effects of AII by angiotensin-converting enzyme (ACE) or angiotensin receptor blocker (ARB) will attenuate these complications. Objective To investigate the effects of ACE/AII inhibitors in long-term PD patients. Patients and Setting We analyzed data from 66 patients treated with PD therapy at our center for at least 2 years, during which time at least 2 standard peritoneal permeability analyses (SPAs) were performed. 36 patients were treated with ACE/AII inhibitors (ACE/ARB group); the other 30 received none of the above drugs during the entire follow-up (control group). The two groups were compared with respect to changes in peritoneal transport over the follow-up time. Results A significant difference in time course of peritoneal transport was found between the 2 groups: in the ACE/ARB group, small solute transport had decreased, while it had increased in the control group. This finding was confirmed by analysis using mixed model for repeated measures. The value of mass transfer area coefficient of creatinine was influenced by the duration of PD therapy (p = 0.017) and this interaction was different with respect to use of ACE/AII inhibitors (p = 0.037). The trend was not found in protein clearances or fluid kinetics. Conclusion Our findings suggest that ACE/AII inhibition is likely to prevent the increase in mass transfer area coefficients that occurs in long-term PD, which is in line with results of experimental animal studies.
Determination of optimal vitamin D3 dosing regimens in HIV-infected paediatric patients using a population pharmacokinetic approach.

AIMS To investigate 25-hydroxycholecalciferol [25(OH)D] population pharmacokinetics in children and adolescents, to establish factors that influence 25(OH)D pharmacokinetics and to assess different vitamin D3 dosing schemes to reach sufficient 25(OH)D concentrations (>30 ng ml(-1) ). METHODS This monocentric prospective study included 91 young HIV-infected patients aged 3 to 24 years. Patients received a 100 000 IU vitamin D3 supplementation. A total of 171 25(OH)D concentrations were used to perform a population pharmacokinetic analysis. RESULTS At baseline 28% of patients had 25(OH)D concentrations below 10 ng ml(-1) , 69% between 10 and 30 ng ml(-1) and 3% above 30 ng ml(-1) . 25(OH)D pharmacokinetics were best described by a one compartment model with an additional production parameter reflecting the input from diet and sun exposure. The effects of skin phototype and bodyweight were significant on 25(OH)D production before any supplementation. The basal level was 27% lower in non-white skin phototype patients and was slightly decreased with bodyweight. No significant differences in 25(OH)D concentrations were related to antiretroviral drugs. To obtain concentrations between 30 and 80 ng ml(-1) , patients with baseline concentrations between 10 and 30 ng ml(-1) should receive 100 000 IU per 3 months. However, vitamin D deficient patients (<10 ng ml(-1) ) would need an intensive phase of 100 000 IU per 2 weeks (two times) followed 2 weeks later by a maintenance phase of 100 000 IU per 3 months. CONCLUSIONS Skin phototype and bodyweight had an influence on the basal production of 25(OH)D. According to 25(OH)D baseline concentrations, dosing schemes to reach sufficient concentrations are proposed.
Do natriuretic peptides modify arterial baroreflexes in sheep?

While atrial and B‐type natriuretic peptides (ANP and BNP) have been shown to enhance reflex responses attributed to cardiac vagal afferents, their effects on arterial baroreceptor reflex function remain controversial. The actions of C‐type natriuretic peptide (CNP) in this regard are unknown. To clarify their actions on arterial baroreflexes, we tested whether i.v. infusions of ANP, BNP or CNP at 10 pmol kg−1 min−1 modified the steady‐state mean arterial blood pressure–heart rate (MAP–HR) relationship in conscious sheep. At this dose, all three natriuretic peptides are known to enhance the cardiac chemoreflex response to phenylbiguanide (Bezold‐Jarisch reflex). Sigmoid MAP–HR relationships were constructed from the steady‐state responses to alternating injections of vasopressor (phenylephrine, 1–15 µg kg−1) and vasodepressor agents (nitroprusside, 1–15 µg kg−1) in the absence and presence of infused ANP, BNP or CNP (tested in random order at least 1 week apart). No parameter of the steady‐state baroreflex relationship was significantly altered by infusion of any of the three natriuretic peptides. We conclude that in conscious sheep, normal arterial baroreceptor–HR reflex function prevails in the presence of moderate doses of ANP, BNP or CNP.
Accuracy of Pedicle Screw Placement in Lumbar Fusions by Plain Radiographs and Computed Tomography

Study Design Postoperative radiographs and computed tomography scans were used to evaluate 74 pedicle screws in 16 consecutive patients who underwent lumbar spine fusion with pedicle screw fixation. Objective To evaluate pedicle screw placement using plain radiographs versus computed tomographic scans. Summary of Background Data Plain radiographs are the primary means of assessing pedicle screw placement. Comparison of plain radiographs and computed tomography has not been done. Methods Screws were graded as IN, OUT, or QUESTIONABLE; the direction of misplacement was noted. All evaluations were performed independently by three observers. Results Fewer screws were clearly within the pedicle on computed tomography when compared with plain radiographs. Computed tomography showed 10 times as many screws violating the medial cortex as did radiographs. Interobserver differences were not statistically significant. Intraobserver differences approached statistical significance when the two tests were compared. No recognized neurologic complications resulted from pedicle screw placement. Conclusions Plain radiographs alone may not accurately reveal pedicle screw placement. Plain radiographs and thin section computed tomographic scans should be used to evaluate postoperative neurologic deficits in patients undergoing instrumented lumbar spine fusion with pedicle screws.
Clinical outcomes of xeno-free autologous cultivated limbal epithelial transplantation: a 10-year study

Purpose Ocular burns can damage the corneal epithelial stem cells located at the limbus. This study evaluated the efficacy of xeno-free autologous cell-based treatment of limbal stem cell deficiency. Methods This retrospective study included 200 patients, above 8 years of age, with clinically diagnosed unilateral total limbal stem cell deficiency due to ocular surface burns treated between 2001 and 2010. A small limbal biopsy was obtained from the unaffected eye. The limbal epithelial cells were expanded ex vivo on human amniotic membrane for 10–14 days using a xeno-free explant culture system. The resulting cultured epithelial monolayer and amniotic membrane substrate were transplanted on to the patient's affected eye. Postoperative corneal surface stability, visual improvement and complications were objectively analysed. Results A completely epithelised, avascular and clinically stable corneal surface was seen in 142 of 200 (71%) eyes at a mean follow-up of 3±1.6 (range: 1–7.6) years. A two-line improvement in visual acuity, without further surgical intervention, was seen in 60.5% of eyes. All donor eyes remained healthy. Conclusions Autologous cultivated limbal epithelial transplantation using a xeno-free explant culture technique was effective in long-term restoration of corneal epithelial stability and improvement of vision in eyes with ocular surface burns.
Paired-pulse stimulation at glutamatergic synapses - pre- and postsynaptic components

Paired-pulse stimulation is a standard protocol that has been used for decades to characterize dynamic systems: the differences in responses to two sequential identical stimuli as a function of inter-stimulus interval provide quantitative information on the dynamics of the system. In neuroscience, the paired-pulse protocol is also widely used at multiple levels of analysis, from behavioral conditioning to synaptic plasticity, and in particular to define the biomolecular mechanism of learning and memory. In a system as small and complex as synapses, it is extremely challenging - if not impossible - to experimentally gain access to the multitude of possible readouts. In the present study, we first introduce a computational synaptic modeling platform that we developed and calibrated based on experimental data from both our laboratories and a variety of publications. We then show how this platform allows not only to replicate experimental data, but also to go beyond technological boundaries and investigate the main parameters responsible for regulation of synaptic transmission and plasticity. The results provide critical information regarding the respective role of various subsynaptic processes and of their interactions. Additionally, this approach can strengthen our understanding of potential dysfunctions (pathologies) and suggest potential approaches to re-establish normal function.
A double-edged sword: the effect of technological advancements in the management of neurotrauma patients

Abstract Introduction: Despite South Africa’s rapidly growing population, the number of patients evaluated by our trauma unit remains static. However, after presentation, increased delays in time to surgery is an issue. With a vast array of technological advancements having been implemented since 2008 at our institution, a clear problem exists at some stage of the patient management process. The aim of this study is to evaluate the efficacy of the management of neurotrauma patients and determine whether there is an association with technological advancements. Methods: An ambispective study was performed to assess the management of neurotrauma patients. A comparative timeline of 7 months (1 January to 31 July 2007 retrospectively and 1 January to 31 July prospectively 2015) was chosen to evaluate several parameters involved in the management of the neurotrauma patient and the factors affecting these. The year 2007 was chosen as this is the last year prior to implementation of technological improvements. Results: The demographics, age group and gender of the respective patient populations was remarkably similar. There was more rapid emergency medical service dispatch and hospital transfer in 2015. The time taken for a patient to get to computed tomography (CT) scan has increased and as has the time period between CT scanning and neurosurgical consultation. Time to ultimate neurosurgical intervention after referral, however, has decreased over the years. Conclusion: One of the greatest sources of delay to surgical management seems to be due to delays in CT scanning where inappropriate prioritization of cases occurs as a result of abuse of the booking and lack of human decision-making and triage. Similarly, after hours needs are not being met with current CT services. As a result of the restriction of human involvement in terms of reviewing scan requests and results there are delays to the neurosurgical service.
Overall Glycemic Index and Glycemic Load of Vegan Diets in Relation to Plasma Lipoproteins and Triacylglycerols

Background: To investigate the overall glycemic index (GI), glycemic load (GL), and intake of dietary fiber, and to examine the associations between these factors and plasma lipoproteins and triacylglycerols in adult vegans in the German Vegan Study (GVS). Methods: Cross-sectional study, Germany. Healthy men (n = 67) and women (n = 87), who fulfilled the study criteria (vegan diet for ≧1 year prior to study start; minimum age of 18 years; no pregnancy/childbirth during the last 12 months) and who participated in all study segments. Results: The average dietary GL of the GVS population was 144, and the average GI was 51.4. The adjusted geometric mean total, HDL, and LDL cholesterol concentrations decreased across the increasing quartiles of GL, carbohydrate and dietary fiber intake. The associations between total cholesterol, HDL cholesterol, LDL cholesterol and GL density and GI were inconsistent. Also, associations between GI, GL, the intake of carbohydrates, and triacylglycerol concentration were not observed. Conclusions: Fiber-rich vegan diets are characterized by a low GI and a low to moderate GL. The data do not support the hypothesis that a carbohydrate-rich diet per se is associated with unfavorable effects on triaclyglycerols that would be predicted to increase the risk of coronary heart disease.
Simple assay based on restriction fragment length polymorphism associated with IL28B in chronic hepatitis C patients

Abstract Objective. Several studies recently revealed that single nucleotide polymorphisms (SNPs) in the interleukin28B (IL28B) region are associated with the response to pegylated interferon-alfa (PEG-IFN-alfa) and ribavirin (RBV) treatment among hepatitis C virus (HCV)-infected individuals of European, African and Asian ancestry. The purpose of the study was to establish methods for determining the SNP rs8099917 associated with IL28B, which might be useful for further research of the treatment of HCV. Material and methods. Blood samples obtained from 93 consecutive patients with chronic hepatitis C were examined. On the basis of the sequence data, a new simple genotyping assay based on a PCR–restriction fragment length polymorphism (RFLP) with two enzymes, BsrDI and Tsp45I, was developed. Results. The proportion of null virological responders in the combined TG/GG group was higher than that in the TT group (p = 0.015), suggesting that minor allele is one of the important factors playing crucial roles in IFN-resistance. Genotyping of rs8099917 by our new method showed results identical to PCR and sequence in 98.9% and 98.9% by BsrDI and Tsp45I, respectively. Using two enzymes, BsrDI and Tsp45I, it was possible to distinguish IL28B SNP rs8099917. Conclusion. This simple method using RFLP will provide the framework for further studies of HCV.
Identification of Two-pore Channel 2 as a Novel Regulator of Osteoclastogenesis*

Background: Two-pore channel 2 (TPC2) is a calcium channel, but its function in osteoclasts is unknown. Results: TPC2 expression levels in osteoclast precursor cells were increased upon osteoclast differentiation induced by RANKL. Down-regulation of TPC2 expression suppressed RANKL-induced intracellular Ca2+ signaling as well as nuclear localization of NFATc1 and inhibited osteoclastogenesis. Conclusion: TPC2 regulates osteoclastogenesis. Significance: TPC2 plays a critical role in osteoclast differentiation. Osteoclast differentiation is one of the critical steps that control bone mass levels in osteoporosis, but the molecules involved in osteoclastogenesis are still incompletely understood. Here, we show that two-pore channel 2 (TPC2) is expressed in osteoclast precursor cells, and its knockdown (TPC2-KD) in these cells suppressed RANKL-induced key events including multinucleation, enhancement of tartrate-resistant acid phosphatase (TRAP) activities, and TRAP mRNA expression levels. With respect to intracellular signaling, TPC2-KD reduced the levels of the RANKL-induced dynamic waving of Ca2+ in RAW cells. The search for the target of TPC2 identified that nuclear localization of NFATc1 is retarded in TPC2-KD cells. Finally, TPC2-KD suppressed osteoclastic pit formation in cultures. We conclude that TPC2 is a novel critical molecule for osteoclastogenesis.
Maternal Serum Placental Protein 13 at Eleven to Thirteen Weeks in Chromosomally Abnormal Pregnancies

Objective: To investigate whether the maternal serum concentration of placental protein 13 (PP13) is altered in chromosomally abnormal pregnancies and to examine the potential value of this placental protein in screening for aneuploidies at 11–13 weeks. Methods: The maternal serum concentration of PP13 at 11–13 weeks was compared in 536 euploid and 134 aneuploid pregnancies (trisomy 21: n = 49; trisomy 18: n = 28; trisomy 13: n = 19; Turner syndrome: n = 28; triploidy: n = 10). Results: Serum PP13, expressed as multiples of the median (MoM) of the euploid group, was not significantly different in trisomy 21 (1.12 MoM) pregnancies, but the levels were decreased in trisomy 18 (0.75 MoM), trisomy 13 (0.65 MoM), Turner syndrome (0.61 MoM) and triploidy (0.19 MoM). In both euploid and aneuploid pregnancies there was a significant association of serum PP13 with both serum pregnancy-associated plasma protein A (PAPP-A) and free β-human chorionic gonadotropin (β-hCG; p < 0.0001 for both). Logistic regression analysis demonstrated that the addition of serum PP13 did not improve the prediction of trisomy 13 and 18 provided by a combination of maternal age, nuchal translucency, and serum free β-hCG and PAPP-A. Conclusion: The measurement of maternal serum PP13 at 11–13 weeks does not improve the performance of screening for aneuploidies achieved by current algorithms.
Lysosome‐associated membrane protein 1 (LAMP‐1) in Alzheimer’s disease

Lysosome‐associated membrane protein 1 (LAMP‐1) is a glycoprotein highly expressed in lysosomal membranes. The present study was initiated to test LAMP‐1 mRNA and protein levels in post mortem frontal cortex (area 8) of Alzheimer’s disease (AD) stages I–IIA/B and stages V–VIC of Braak and Braak, compared with age‐matched controls. TaqMan PCR assays and Western blots demonstrated upregulation of LAMP‐1 mRNA and protein in the cerebral cortex in ADVC. In addition, immunohistochemical studies have shown increased LAMP‐1 immunoreactivity in neurones, and in glial cells surrounding senile plaques, in AD cases. Interestingly, LAMP‐1 immunoreactivity has little correlation with phosphorylated tau deposition and neurofibrillary tangles (NFTs), as neurones with NFTs were rarely LAMP‐1 immunoreactive. In contrast, LAMP‐1 expression was enhanced in neurones with granulovacuolar degeneration. Finally, LAMP‐1 occurred in microglia and multinucleated giant cells in one AD case in whom amyloid burden was cleared following βA‐peptide immunization. These findings support the participation of lysosomes in βA‐amyloid and, probably, in hyperphosphorylated tau turnover in AD.