Miracle-dz/UniFAR-FTUs huggingface dataset:
A porcine model: surgical anatomy of the orbit for maxillofacial surgery

Due to its similarity to humans, the pig has proven to be a suitable biomodel for both research purposes and for training medical professionals, particularly in surgical specializations. For example, new implant materials have been tested on pig jaws and pigs have also been used in the development of new surgical techniques. For optimizing the effectiveness of such research or training, detailed data on the anatomy of their particular features are needed. At present, however, only limited information related to surgical and imaging anatomy of the facial and orbital areas of the pig and its comparison to human structures from the experimental surgery point of view is available in the literature. The aim of this study was to obtain such data and to compare the morphological structures of the porcine and human orbital regions and to lay down the foundation for practical use in experimental surgery. Ten pig heads were examined using computed tomography (CT) and magnetic resonance imaging (MRI) and, subsequently, a dissection of the orbit was carried out. Attention was focused on the structure of the orbit (floor, rim and nerves) frequently affected by pathological processes in humans (such as trauma, infection or tumours) and which consequently are frequently the subject of maxillofacial surgery. The porcine orbit is suitable for use in experimental medicine. However, if used in experiments, its anatomical peculiarities must be taken into consideration. Our study presents a foundation of basic knowledge for researchers who plan to use the pig as a biomedical model to investigate alternative treatments in the head region.
Developments in Quantitative PCR

Abstract In recent years the growing interest in quantitative applications of the polymerase chain reaction (PCR) has favoured the development of a large number of assay procedures suitable for this purpose. In this paper we review some basic principles of quantitative PCR and in particular the role of reference materials and calibrators and the different strategies adopted for nucleic acid quantification. We focus on two methodological approaches for quantitative PCR in this review: competitive PCR and real-time quantitative PCR based on the use of fluorogenic probes. The first is one of the most common methods of quantitative PCR and we discuss the structure of the competitors and the various assay procedures. The second section is dedicated to a recent promising technology for quantitative PCR in which the use of fluorogenic probes and dedicated instrumentation allows the development of homogeneous methods. Assay performance of these methods in terms of practicability and reliability indicates that these kinds of technologies will have a widespread use in the clinical laboratory in the near future.
Cyclic AMP‐dependent protein kinases from Balb 3T3 cells and other 3T3 derived lines

Cyclic AMP‐dependent protein kinase and 3H‐cAMP‐binding activities were determined in normal Balb 3T3 cells and compared with the same preparations from SV40, chemical, and spontaneous transformants of 3T3 cells. The cytosolic protein kinase activities and protein kinase activity ratios were similar in all cell lines, although when the normal 3T3 cytosol was prepared by homogenization it contained less 3H‐cAMP binding activity than the transformed 3T3 cytosols. The Triton X‐100 treated particulate fractions from the normal and transformed 3T3 cells contained similar protein kinase and binding activities.
Cancer Incidence Among Canadian Kidney Transplant Recipients

A number of studies have observed increased cancer incidence rates among individuals who have received renal transplants. Generally, however, these studies have been limited by relatively small sample sizes, short follow‐up intervals or focused on only one cancer site. We conducted a nationwide population‐based study of 11,155 patients who underwent kidney transplantation between 1981 and 1998. Incident cancers were identified up to December 31, 1999, through record linkage to the Canadian Cancer Registry. Patterns of cancer incidence in the cohort were compared to the Canadian general population using standardized incidence ratios (SIRs). We examined variations in risk according time since transplantation, year of transplantation and age at transplantation. In our patient population, we observed a total of 778 incident cancers versus 313.2 expected (SIR = 2.5, 95% CI = 2.3–2.7). Site‐specific SIRs were highest for cancer of the lip (SIR = 31.3, 95% CI = 23.5–40.8), non‐Hodgkin's lymphoma (NHL) (SIR = 8.8, 95% CI = 7.4–10.5), and kidney cancer (SIR = 7.3, 95% CI = 5.7–9.2). SIRs for NHL and cancer of the lip and kidney were highest and among transplant patients. This study confirms previous findings of increased risks of posttransplant cancer. Our findings underscore the need for increased vigilance among kidney transplant recipients for cancers at sites where there are no population‐based screening programs in place.
Rho GTPase independent regulation of ATM activation and cell survival by the RhoGEF Net1A

ATM activation following DNA damage is a critical event which is required for efficient DNA repair and cell survival, yet signaling mechanisms controlling its activation are incompletely understood. The RhoGEF Net1 has previously been reported to control Rho GTPase activation and downstream cell survival outcomes following double strand DNA damage. However the role of Net1 isoforms in controlling ATM-dependent cell signaling has not been assessed. In the present work we show that expression of the Net1A isoform is specifically required for efficient activation of ATM but not the related kinase DNA-PK after ionizing radiation. Surprisingly Net1A overexpression also potently suppresses ATM activation and phosphorylation of its substrate H2AX. This effect does not require catalytic activity towards RhoA or RhoB, and neither Rho GTPase affects ATM activation, on its own. Consistent with a role in controlling ATM activation, Net1A knockdown also impairs DNA repair and cell survival. Taken together these data indicate that Net1A plays a plays a previously unrecognized, Rho GTPase-independent role in controlling ATM activity and downstream signaling after DNA damage to impact cell survival.
Functional domains required for tat‐induced transcriptional activation of the HIV‐1 long terminal repeat.

The transcriptional regulation of the human immunodeficiency virus (HIV) type I involves the interaction of both viral and cellular proteins. The viral protein tat is important in increasing the amount of viral steady‐state mRNA and may also play a role in regulating the translational efficiency of viral mRNA. To identify distinct functional domains of tat, oligonucleotide‐directed mutagenesis of the tat gene was performed. Point mutations of cysteine residues in three of the four Cys‐X‐X‐Cys sequences in the tat protein resulted in a marked decrease in transcriptional activation of the HIV long terminal repeat. Point mutations which altered the basic C‐domain of the protein also resulted in decreases in transcriptional activity, as did a series of mutations that repositioned either the N or C termini of the protein. Conservative mutations of other amino acids in the cysteine‐rich or basic regions and in a series of proline residues in the N terminus of the molecule resulted in minimal changes in tat activation. These results suggest that several domains of tat protein are involved in transcriptional activation with the cysteine‐rich domain being required for complete activity of the tat protein.
Clinical Variability in Rett Syndrome

The clinical variability of Rett syndrome, associated with mutations in the MECP2 gene, varies from classically symptomatic female patients to asymptomatic female patients, and male patients who have none of the diagnostic features considered pathognomonic of this disease. Multiple factors contribute to this variability. In our studies, mutations closer to the amino-terminus, prior to amino acid 255, led to severe clinical manifestations, such as inability to walk, severe dysphagia, and urinary organic acid abnormalities, compared with mutations toward the carboxyl-terminus. However, we found no correlation between severity and mutation type (missense versus nonsense). Despite the importance of mutation location to clinical severity, the widely varying severity within the same mutation suggests that in females, X-chromosome inactivation or other epigenetic phenomena also have roles in determining severity. We propose that stages 1 and 2 of the disease are a consequence of failed, time-linked, postnatal expression of MeCP2 in cerebellar neurons. This, in association with glutamate N-methyl-D-aspartate receptor—mediated neuroexcitotoxic injury to the differentiating neurons, results in the transient age-specific autistic-like behavior, motor, and cognitive dysfunction associated with these stages. (J Child Neurol 2003; 18:662-668).
Continuous Infusion of Bupivacaine for Pain Control after Anterior Iliac Crest Bone Grafting for Alveolar Cleft Repair in Children

Objective The purpose of this study was (1) to evaluate the analgesic efficacy of continuous infusion bupivacaine, (2) to evaluate the effects of the site-specific catheter infusion on operating room time, narcotic use, ambulatory status, and length of hospitalization, (3) to monitor for adverse outcomes, and (4) to assess patient/family acceptance. Design Randomized, double-blinded, and prospective study of bupivacaine versus saline for pain control after anterior iliac crest bone grafting for alveolar cleft repair. Setting University of Alabama at Birmingham. Patients A total of 65 pediatric patients with alveolar cleft defects treated between 2006 and 2009. Interventions Anterior iliac crest bone grafting for alveolar cleft repair with assignment to either a bupivacaine or a saline infusion group. Main Outcome Measures Physical examination, pain ratings, narcotic use, ambulatory status, operating room time, and length of hospital stay. Results On the blinded physical exam, 71% in the bupivacaine infusion group and 42% in the saline infusion group were assessed as not experiencing pain at the surgical hip site. The experimental group used less narcotics compared with the control group. No significant differences were noted with operating room time, initial ambulatory status, or length of hospitalization (1.09 versus 1.12 days). Satisfaction and acceptance of the catheter treatment was universal. Conclusions These results suggest that postoperative infusion of bupivacaine may be efficacious for enhancing pain relief after bone harvest in pediatric patients and may enhance parental perceptions of postoperative care; however, this patient population is difficult to study accurately.
Expression of Endoplasmic Reticulum Aminopeptidases in EBV-B Cell Lines from Healthy Donors and in Leukemia/Lymphoma, Carcinoma, and Melanoma Cell Lines1

Peptide trimming in the endoplasmic reticulum (ER), the final step required for the generation of most HLA class I-binding peptides, implicates the concerted action of two aminopeptidases, ERAP1 and ERAP2. Because defects in the expression of these peptidases could lead to aberrant surface HLA class I expression in tumor cells, we quantitatively assayed 14 EBV-B cell lines and 35 human tumor cell lines of various lineages for: 1) expression and enzymatic activities of ERAP1 and ERAP2; 2) ER peptide-trimming activity in microsomes; 3) expression of HLA class I H chains and TAP1; and 4) surface HLA class I expression. ERAP1 and ERAP2 expression was detectable in all of the EBV-B and tumor cell lines, but in the latter it was extremely variable, sometimes barely detectable, and not coordinated. The expression of the two aminopeptidases corresponded well to the respective enzymatic activities in most cell lines. A peptide-trimming assay in microsomes revealed additional enzymatic activities, presumably contributed by other unidentified aminopeptidases sharing substrate specificity with ERAP2. Interestingly, surface HLA class I expression showed significant correlation with ERAP1 activity, but not with the activity of either ERAP2 or other unidentified aminopeptidases. Transfection with ERAP1 or ERAP2 of two tumor cell lines selected for simultaneous low expression of the two aminopeptidases resulted in the expected, moderate increases of class I surface expression. Thus, low and/or imbalanced expression of ERAP1 and probably ERAP2 may cause improper Ag processing and favor tumor escape from the immune surveillance.
The Association of Serum Vitamin D Concentration with Serious Complications After Noncardiac Surgery

BACKGROUND:Vitamin D deficiency is a global health problem. Epidemiological studies demonstrate that vitamin D is both cardioprotective and neuroprotective. Vitamin D also plays a substantial role in innate and acquired immunity. Our goal was to evaluate the association of serum vitamin D concentration on serious postoperative complications and death in noncardiac surgical patients. METHODS:We retrospectively analyzed the data of 3509 patients who had noncardiac surgery at the Cleveland Clinic Main Campus and had a serum vitamin D measurement. The relationship between serum vitamin D concentration and all-cause in-hospital mortality, in-hospital cardiovascular morbidity, and serious in-hospital infections was assessed as a common effect odds ratio (OR) by using a multivariate generalized estimating equation model with adjustment for demographic, medical history variables, and type and duration of surgery. RESULTS:Higher vitamin D concentrations were associated with decreased odds of in-hospital mortality/morbidity (P = 0.003). There was a linear reduction of the corresponding common effect odds ratio (OR 0.93, 95% confidence interval, 0.88–0.97) for severe in-hospital outcomes for each 5 ng/mL increase in vitamin D concentration over the range from 4 to 44 ng/mL. In addition, we found that the odds versus patients with vitamin D <13 ng/mL (i.e., 1st quintile) were significantly lower in patients with vitamin D 13–20, 20–27, 27–36, and > 36 ng/mL (i.e., 2nd–5th quintiles); the corresponding estimated ORs were 0.65 (99% confidence interval, 0.43–0.98), 0.53 (0.35–0.80), 0.44 (0.28–0.70), and 0.49 (0.31–0.78), respectively. However, there was no statistically significant difference among individual quintiles >13 ng/mL. CONCLUSIONS:Vitamin D concentrations were associated with a composite of in-hospital death, serious infections, and serious cardiovascular events in patients recovering from noncardiac surgery. While causality cannot be determined from our retrospective analysis, the association suggests that a large randomized trial of preoperative vitamin D supplementation and postoperative outcomes is warranted.
Characterization of the Central Metabolic Pathways in Thermoanaerobacter sp. Strain X514 via Isotopomer-Assisted Metabolite Analysis

ABSTRACT Thermoanaerobacter sp. strain X514 has great potential in biotechnology due to its capacity to ferment a range of C5 and C6 sugars to ethanol and other metabolites under thermophilic conditions. This study investigated the central metabolism of strain X514 via 13C-labeled tracer experiments using either glucose or pyruvate as both carbon and energy sources. X514 grew on minimal medium and thus contains complete biosynthesis pathways for all macromolecule building blocks. Based on genome annotation and isotopic analysis of amino acids, three observations can be obtained about the central metabolic pathways in X514. First, the oxidative pentose phosphate pathway in X514 is not functional, and the tricarboxylic acid cycle is incomplete under fermentative growth conditions. Second, X514 contains (Re)-type citrate synthase activity, although no gene homologous to the recently characterized (Re)-type citrate synthase of Clostridium kluyveri was found. Third, the isoleucine in X514 is derived from acetyl coenzyme A and pyruvate via the citramalate pathway rather than being synthesized from threonine via threonine ammonia-lyase. The functionality of the citramalate synthase gene (cimA [Teth514_1204]) has been confirmed by enzymatic activity assays, while the presence of intracellular citramalate has been detected by mass spectrometry. This study demonstrates the merits of combining 13C-assisted metabolite analysis, enzyme assays, and metabolite detection not only to examine genome sequence annotations but also to discover novel enzyme activities.
New frontiers in androgen biosynthesis and metabolism

Purpose of reviewTo summarize recent advances in androgen biosynthesis and metabolism in peripheral tissues (e.g., liver and prostate) and how these can be exploited therapeutically. Recent findingsHuman liver catalyzes the reduction of circulating testosterone to yield four stereoisomeric tetrahydrosteroids. Recent advances have assigned the enzymes responsible for these reactions and elucidated their structural biology. Data also suggest that for 5α-dihydrotestosterone (5α-DHT), conjugation reactions (phase II) may precede ketosteroid reduction (phase I) reactions. Human prostate is the site of benign prostatic hyperplasia and prostate cancer, which occur in the aging male. Although the importance of local androgen biosynthesis in these diseases is accepted, recent advances have identified enzymes that regulate ligand access to the androgen-receptor; a ‘backdoor pathway’ to 5α-DHT that does not require testosterone acting as an intermediate; and the finding that castrate-resistant prostate cancer (CRPC) has undergone an adaptive response to androgen deprivation, which involves intratumoral testosterone and 5α-DHT biosynthesis that can be targeted using inhibitors of (CYP17-hydroxylase/17,20-lyase), aldo-keto reductase 1C3, and 5α-reductase type 1 and type 2. SummaryEnzyme isoforms responsible for the biosynthesis and metabolism of androgens in liver and prostate have been identified and those responsible for the biosynthesis of androgens in CRPC can be therapeutically targeted.
Maximal Potential Patent Foramen Diameter Does Not Correlate with the Type or Frequency of the Neurologic Event prior to Closure

Background: We analyzed our data on patients undergoing transcatheter patent foramen ovale (PFO) closure to determine if the maximal potential PFO diameter (MPPD) by balloon sizing correlates with important clinical characteristics in this population. Methods: We defined stroke as a focal neurologic deficit lasting >24 h, or focal deficit of shorter duration associated with permanent MRI/CT changes consistent with a focal infarction. Parameters analyzed included age, gender, anticoagulation, hypertension, smoking, MRI/CT findings and MPPD at catheterization. We specifically analyzed the type of neurologic event (stroke/transient ischemic attack, TIA), and number of recorded preceding clinical neurologic events. Results: In 216 consecutive patients, 167 suffered a stroke. MRI/CT changes consistent with one or more embolic events were seen in 156 patients; 49 had a clinical TIA. There was no significant difference in MPPD between stroke (11.0 ± 3.6 mm) and TIA groups (10.9 ± 3.9 mm; 95% confidence interval for difference: –1.33 to 1.00). MPPD did not differ between MRI/CT-positive vs. -negative strokes, and had no correlation with the number of identified pre-closure clinical neurologic events. Conclusions: Continued investigation is needed to determine whether other PFO characteristics, or other anatomic/physiologic parameters, may be useful to identify patients at high risk for cryptogenic stroke/TIA, even before they have their first neurologic event.
Surgical treatment of independent bitemporal lobe epilepsy defined by invasive recordings

Objectives: Bitemporal lobe epilepsy is commonly encountered in the evaluation of pharmacoresistant epilepsy. Yet the role of surgery in the management of these patients is unclear. This study evaluates the impact of surgery on seizure tendency and quality of life, as well as prognostic indicators in individuals with proven ictal onset bitemporal lobe epilepsy. Methods: The study population comprised all patients who underwent temporal lobe surgery over a 10 year period and had ictal onset bitemporal lobe epilepsy identified with intracranial electrode monitoring. Patients with extratemporal seizure generators were excluded. Subjects were divided into a favourable or less favourable group based on the results of surgery on seizure tendency. Results: 11 subjects were studied with a mean 5.9 years of post-surgical follow-up. Six subjects constituted the favourable outcome group. Four had a less favourable outcome and continued to have frequent seizures after surgery; however, three with less favourable seizure reduction subjectively reported improvement in quality of life after surgery as a result of reduced seizure frequency and severity, and reduced medications. No single preoperative factor was significantly different between the groups, including ictal EEG laterality, epilepsy duration, age at surgery, age at seizure onset and mesial temporal atrophy. Conclusions: Surgical resection is an important treatment option for medically intractable bitemporal epilepsy. The proportion of seizures arising from one temporal lobe is not reliable as a single indicator to prognosticate the results of surgery on seizure tendency. In addition, individuals who achieved only palliation by reducing seizure frequency experienced improvement in quality of life.
Antagonistic regulation of Cyp26b1 by transcription factors SOX9/SF1 and FOXL2 during gonadal development in mice

Sex determination in fetal germ cells depends on a balance between exposure to retinoic acid (RA) and the degradation of RA achieved by the testis‐specific expression of the catabolic cytochrome P450 enzyme, CYP26B1. Therefore, identification of factors regulating the expression of the Cyp26b1 gene is an important goal in reproductive biology. We used in situ hybridization to demonstrate that Cyp26b1 and transcription factor genes steroidogenic factor‐1 (Sf1) and Sry‐related HMG box 9 (Sox9) are coexpressed in Sertoli cells, whereas Cyp26b1 and Sf1 are coexpressed in Leydig cells in mouse fetal testes. In the mouse gonadal somatic cell line TM3, transfection of constructs expressing SOX9 and SF1 activated Cyp26b1 expression, independently of the positive regulator RA. In embryonic gonads deficient in SOX9 or SF1, Cyp26b1 expression was decreased relative to wild‐type (WT) controls, as measured by quantitative RT‐PCR (qRT‐PCR). Furthermore, qRT‐PCR showed that Cyp26b1 up‐regulation by SOX9/SF1 was attenuated by the ovarian transcription factor Forkhead box L2 (FOXL2) in TM3 cells, whereas in Foxl2‐null mice, Cyp26b1 expression in XX gonads was increased ~20‐fold relative to WT controls. These data support the hypothesis that SOX9 and SF1 ensure the male fate of germ cells by up‐regulating Cyp26b1 and that FOXL2 acts to antagonize Cyp26b1 expression in ovaries. —Kashimada, K. , Svingen, T. , Feng, C. ‐W. , Pelosi, E. , Bagheri‐Fam, S. , Harley, V. R. , Schlessinger, D. , Bowles, J., Koopman, P. Antagonistic regulation of Cyp26b1 by transcription factors SOX9/SF1 and FOXL2 during gonadal development in mice. FASEB J. 25, 3561–3569 (2011). www.fasebj. org