Miracle-dz/UniFAR-FTUs huggingface dataset:
Bypasses in intracellular glucose metabolism in iron‐limited Pseudomonas putida

Decreased biomass growth in iron (Fe)‐limited Pseudomonas is generally attributed to downregulated expression of Fe‐requiring proteins accompanied by an increase in siderophore biosynthesis. Here, we applied a stable isotope‐assisted metabolomics approach to explore the underlying carbon metabolism in glucose‐grown Pseudomonas putida KT2440. Compared to Fe‐replete cells, Fe‐limited cells exhibited a sixfold reduction in growth rate but the glucose uptake rate was only halved, implying an imbalance between glucose uptake and biomass growth. This imbalance could not be explained by carbon loss via siderophore production, which accounted for only 10% of the carbon‐equivalent glucose uptake. In lieu of the classic glycolytic pathway, the Entner–Doudoroff (ED) pathway in Pseudomonas is the principal route for glucose catabolism following glucose oxidation to gluconate. Remarkably, gluconate secretion represented 44% of the glucose uptake in Fe‐limited cells but only 2% in Fe‐replete cells. Metabolic 13C flux analysis and intracellular metabolite levels under Fe limitation indicated a decrease in carbon fluxes through the ED pathway and through Fe‐containing metabolic enzymes. The secreted siderophore was found to promote dissolution of Fe‐bearing minerals to a greater extent than the high extracellular gluconate. In sum, bypasses in the Fe‐limited glucose metabolism were achieved to promote Fe availability via siderophore secretion and to reroute excess carbon influx via enhanced gluconate secretion.
Tumor angiogenesis is an independent prognostic indicator in primary breast carcinoma

Clinical importance of tumor angiogenesis, especially its significance as a prognostic indicator, was examined in 125 primary breast‐cancer patients. The grade of neovascularization was assessed by the vessel density which was obtained by immunocytochemical staining for factor VIII antigen. Postoperative survey demonstrated that the vessel density is a statistically significant predictor of relapse‐free survival (median follow‐up period: 62 months). Patients with over 100 counts of factor‐VIII antigen‐positive cells per 200 x field in the most active areas of neovascularization showed significantly poorer prognosis than those with less than 100 counts. The prognostic value of the vessel density was also confirmed by another evaluation method using immunocytochemical staining to CD‐31 which is a platelet/endothelial cell adhesion molecule. A significant difference in relapse‐free survival rate was shown between patients having higher counts of CD‐31 positive cells and those having lower counts. Breakdown analysis stratified by nodal status showed that the vessel density was a significant prognostic indicator in node‐negative and node‐positive patients. Multivariate analysis indicated that the vessel density is an independent prognostic indicator in primary breast‐cancer patients.
VASODILATORY ACTIVITY OF NOVEL CARBAMATE DERIVATIVES OF ISATIN

1 Isatin (1H‐indole‐2,3 dione) is an endogenous compound that may act as a physiological regulator of muscle contraction by reducing cGMP production by inhibition of guanylyl cyclase (GC) activity. 2 Intracellular cGMP levels can regulate the contractile response of smooth muscle. Therefore, in the present study we investigated the effects of seven novel carbamate derivatives of isatin, namely C1–C7, on the contractility of aortic rings from Wistar rats. 3 Carbamates C1 and C6 most effectively promoted endothelium‐dependent relaxation of aortic rings pretreated with 10 µmol/L phenylephrine (PE) to induce contraction. The concentration of the C1 and C6 carbamates necessary to reduce PE‐induced aortic contraction by 50% (IC50) was 5.6 ± 1.0 and 48.4 ± 3.4 µmol/L, respectively. Carbamate derivative‐induced vasodilation required an intact endothelium, which is responsible for nitric oxide (NO) release. 4 Pretreatment of rings with 100 µmol/L naloxone or 10 µmol/L atropine prevented the C1‐ and C6‐mediated vascular relaxation, indicating that the vasodilatory activity was dependent on the activation of opioid or muscarinic receptors, respectively. 5 The results of our studies provide insights into the role of novel carbamates in the regulation of vascular tone. Carbamates could stimulate NO synthesis, which induces vasodilation primarily by stimulation of GC and cGMP production. Taken together, our findings suggest that carbamate derivative‐induced vasodilation may be considered an alternative treatment for primary and/or secondary hypertension.
Pulmonary pathology of rapidly fatal transfusion‐related acute lung injury reveals minimal evidence of diffuse alveolar damage or alveolar granulocyte infiltration

BACKGROUND: Transfusion‐related acute lung injury (TRALI) is the leading cause of transfusion‐associated death in the United States. Its diagnosis is based on clinical and radiographic changes that are indistinguishable from acute lung injury/acute respiratory distress syndrome (ALI/ARDS). TRALI is presumed to be a form of ALI/ARDS; however, it differs in its triggering events and associated mortality. Two cases of rapidly fatal TRALI in which the postmortem pathology differed from that classically associated with ALI/ARDS are reported.
Polyphenolic Nutrients in Cancer Chemoprevention and Metastasis: Role of the Epithelial-to-Mesenchymal (EMT) Pathway

The epithelial-to-mesenchymal transition (EMT) has received significant interest as a novel target in cancer prevention, metastasis, and resistance. The conversion of cells from an epithelial, adhesive state to a mesenchymal, motile state is one of the key events in the development of cancer metastasis. Polyphenols have been reported to be efficacious in the prevention of cancer and reversing cancer progression. Recently, the antimetastatic efficacy of polyphenols has been reported, thereby expanding the potential use of these compounds beyond chemoprevention. Polyphenols may affect EMT pathways, which are involved in cancer metastasis; for example, polyphenols increase the levels of epithelial markers, but downregulate the mesenchymal markers. Polyphenols also alter the level of expression and functionality of important proteins in other signaling pathways that control cellular mesenchymal characteristics. However, the specific proteins that are directly affected by polyphenols in these signaling pathways remain to be elucidated. The aim of this review is to analyze current evidence regarding the role of polyphenols in attenuating EMT-mediated cancer progression and metastasis. We also discuss the role of the most important polyphenol subclasses and members of the polyphenols in reversing metastasis and targeting EMT. Finally, limitations and future directions to improve our understanding in this field are discussed.
Effects of long-term vitamin E supplementation in alcoholic cirrhotics.

OBJECTIVE Alcohol ingestion promotes lipoperoxidation and alters cellular antioxidant mechanisms. Alpha-tocopherol levels decrease in alcoholics as severity of liver damage increases. The aim of this protocol was to study the effects of a long-term oral 500 mg vitamin E daily supplementation in decompensated ambulatory alcoholic cirrhotics. PATIENTS AND METHODS 67 subjects were included in this double blind trial; 33 patients received vitamin E and 34 patients received placebo tablets of identical appearance during 1 year. Each month, the patients were seen by a nurse practitioner who was in charge of detecting alcohol ingestion and checking adherence to treatment. Every 3 months, the patients underwent a medical examination, and blood samples were taken for clinical laboratory analysis and serum vitamin E measurement. RESULTS Alpha-tocopherol levels were significantly lower in patients with more severe liver disease. This difference was not significant when vitamin E levels were corrected by cholesterol. Oral supplementation significantly increased serum vitamin E levels in the experimental group. Alcohol ingestion and hospitalization rates were similar in both groups. Life table analysis did not show significant differences in mortality between the two groups. DISCUSSION Vitamin E supplementation with adequate doses of an alpha-tocopheryl acetate formulation during 1 year did not influence hepatic laboratory parameters, mortality or hospitalization rates of decompensated alcoholic cirrhotics, although serum levels of the vitamin significantly increased.
An Evaluation of Linear Model Analysis Techniques for Processing Images of Microcirculation Activity

Sequences of images of the cortical surface can be processed to reveal information about the cortical microcirculation, regional cerebral blood flow (rCBF), and changes induced by neuronal activity. This study examined the use of different analysis methodologies on intrinsic optical images taken from rat sensory motor cortex and testes. Generalized linear model (GLM) analysis was used and compared with standard signal processing methods including principal component analysis. The GLM method has been used by Friston et al. (1994, Hum. Brain Map., 1: 214-220) in the analysis of functional magnetic resonance imagery to identify regions of focal activity. We investigated the use of this method to analyze video image data of the modulation of rCBF from rat cortex. The results revealed spatiotemporal variations in rCBF in response to stimulation within local regions of cortex. The advantage of the GLM method is that it augments ordinary signal processing methods with an estimate of statistical reliability. The use of different wavelengths of illumination reveals spatial structures with different temporal relationships. In image time series data collected under green and red illumination a phase difference was found in the low frequency approximately 0.1 Hz vasomotion oscillation. This phase difference occurred in data from both cortex and testes. A possible explanation of these differences is that the spectral absorption characteristics of the tissue reflect changes in the volume proportions of the different hemoglobin derivatives in interacting with the modulation of the volume of blood. It is suggested that the combination of these effects produces the phase differences we detect.
Sustainable use of continuous positive airway pressure in extremely preterm infants during the first week after delivery

Background: Early use of nasal continuous positive airway pressure (nCPAP) may reduce lung damage, but it is not clear how many extremely preterm infants can be cared for without mechanical ventilation on the first days after delivery. Objectives: To describe our experience of nCPAP in infants born at <27 weeks’ gestation and to determine the chance of reintubation of this group of extremely preterm infants. Methods: A retrospective, observational study examined the period from November 2002 to October 2003, when efforts were made to extubate infants to nCPAP at the earliest opportunity. Data were collected on all infants born at <27 weeks’ and gestation admitted to The Neonatal Intensive Care Unit, Queen Charlotte’s and Chelsea Hospital, London, UK. The chance of an individual infant requiring reintubation within 48 h of delivery was estimated, calculating the predictive probability using a Bayesian approach, and oxygen requirements at 36 weeks’ postmenstrual age were examined. Results: 60 infants, 34 inborn and 26 ex utero transfers, were admitted; 7 infants admitted 24 h after birth were excluded and 5 died within 48 h. The mean birth weight was 788 g and the gestational age was 25.3 weeks. Extubation was attempted on day 1 in 21 of 52 infants on ventilators and was successful in 14; and on day 2 in 14 of 35 and successful in 10 of infants extubated within 48 h of delivery survived to discharge. 5 of 23 infants on mechanical ventilation at 48 h of age were on air at 36 weeks postmenstrual age, and 12 of 26 of those were on nCPAP at 48 h of age. The probability of an individual baby remaining on nCPAP was 66% (95% CI 46% to 86%) on day 1 and 80% (95% CI 60% to 99%) on day 2. The smallest infant to be successfully extubated was 660 g and the youngest gestational age was 23.8 weeks. Conclusions: Extremely preterm infants can be extubated to nCPAP soon after delivery, with a reasonable probability of not requiring immediate reintubation.
Rejection Reversibly Alters Enteroendocrine Cell Renewal in the Transplanted Small Intestine

Acute small intestinal allograft rejection presents clinically as an abrupt increase in ileal fluid output in the absence of extensive inflammation. We questioned whether acute intestinal rejection might be accompanied by a disturbance of normal intestinal stem cell differentiation. We examined the intestinal epithelial secretory cell lineage among patients experiencing early rejection before and during rejection as well as following corrective therapy. Lineage‐specific progenitors were identified by their expression of stage‐specific transcription factors. Progenitors of the enteroendocrine cell (EEC) expressing neurogenin‐3 (NEUROG3) were found to be disproportionately reduced in numbers, along with their more mature EEC derivatives expressing neuro D; the enteric hormone PYY was the most profoundly depleted of all the EEC products evaluated. No change in the numbers of goblet or Paneth cells was observed. Steroid treatment resulted in resolution of clinical symptoms, restoration of normal patterns of EEC differentiation and recovery of normal levels of enteric hormones. Acute intestinal rejection is associated with a loss of certain subtypes of EEC, most profoundly, those expressing PYY. Deficiency of the mature EECs appears to occur as a consequence of a mechanism that depletes NEUROG3 EEC progenitors. Our study highlights the dynamics of the EEC lineage during acute intestinal rejection.
Monitoring of regional tissue oxygenation with near-infrared spectroscopy during the early postoperative course after superior cavopulmonary anastomosis.

OBJECTIVES Near-infrared spectroscopy (NIRS) offers continuous non-invasive monitoring of regional tissue oxygenation. We evaluated NIRS monitoring during the postoperative course after superior cavopulmonary anastomosis in patients with hypoplastic left heart syndrome and anatomically related malformations. METHODS Cerebral (cSO(2)) and somatic (sSO(2)) tissue oxygenations were recorded for 48 h and compared with routine measures of intensive care monitoring. Changes in parameters in the case of postoperative complications were evaluated. RESULTS Data were obtained from 32 patients. Median age at operation was 2.9 (1.5-10.0) months and weight was 5.3 ± 1.0 kg. Postoperative complications occurred in 7 patients (pulmonary artery thrombus n = 4, pneumothorax n = 1, cardiopulmonary resuscitation n = 1 and low-cardiac output n = 1). cSO(2) was 44 ± 14% at the end of the operation and reached its minimum of 40 ± 11% 2 h later (P = 0.018). Overall, cSO(2) was depressed early after surgery and increased from a mean of 42 ± 11% during the first 4 postoperative hours to 57 ± 8% in the last 4 h of the study period (P < 0.001). The sSO(2) decreased from 77 ± 11% during the early postoperative course to 68 ± 9% within the later course (P < 0.001). The cSO(2) correlated with the arterial partial pressure of oxygen (pO(2), r = 0.364, P < 0.001), with the arterial oxygen saturation (SaO(2), r = 0.547, P < 0.001) and with the central venous oxygen saturation providing the strongest correlation (SvO(2), r = 0.686, P < 0.001). Analysis of agreement between cSO(2) and SvO(2) measurements revealed a mean bias of 0.97 with limits of agreement between 19.8 and -17.9%. Inclusion of both cSO(2) and sSO(2) into a linear regression model slightly improved the prediction of SvO(2) from NIRS values (r = 0.706, P < 0.001). The mean values of cSO(2), sSO(2), SaO(2) and SvO(2) during the early postoperative period were lower in patients with complications (cSO(2): 45 ± 9 vs 29 ± 5%, P < 0.001; sSO(2): 80 ± 11 vs 70 ± 6%, P = 0.004; SaO(2): 76 ± 8 vs 66 ± 6%, P = 0.004; SvO(2): 48 ± 14 vs 32 ± 6%, P < 0.001). CONCLUSIONS NIRS technology allows inferring the global oxygenation from continuous non-invasive measurements of regional tissue oxygenation. The cSO(2) is lowered in the early postoperative course. Lower cSO(2) values in the early postoperative course may be predictive of postoperative complications.
Baseline Viral Load and Immune Activation Determine the Extent of Reconstitution of Innate Immune Effectors in HIV-1-Infected Subjects Undergoing Antiretroviral Treatment12

We analyzed dendritic cell (DC) and NK cell compartments in relation to CD4 recovery in 21 HIV-infected subjects followed to <50 copies/ml once starting antiretroviral therapy (ART) and observed for 52 wk of sustained suppression. Although CD4 counts increased in all subjects in response to ART, we observed a restoration of functional plasmacytoid DC (PDC) after 52 wk of sustained suppression under ART (from 1850 cells/ml to 4550 cells/ml) to levels comparable to controls (5120 cells/ml) only in subjects with a low baseline viral load, which also rapidly suppressed to <50 copies/ml upon ≤60 days from ART initiation. Recovery of PDC at week 52 correlates with level of CD95 expression on CD8 T cells and PDC frequency following first ART suppression. NK cytotoxic activity increased rapidly upon viral suppression (VS) and correlated with PDC function at week 52. However, restoration of total NK cells was incomplete even after 52 wk on ART (73 cells/μl vs 122 cells/μl in controls). Direct reconstitution experiments indicate that NK cytotoxic activity against virally infected target cells requires DC/NK cooperation, and can be recovered upon sustained VS and recovery of functional PDC (but not myeloid DC) from ART-suppressed subjects. Our data indicate that viremic HIV-infected subjects may have different levels of reconstitution of DC and NK-mediated function following ART, with subjects with lower initial viremia and the greatest reduction of baseline immune activation at VS achieving the greatest level of innate effector cell reconstitution.
Fate of mesenchymal stem cells transplanted to osteonecrosis of femoral head

The purpose of this study was to investigate the survival and differentiation status of MSCs transplanted to ONFH. Traumatic ONFH was surgically produced in skeletally mature mongrel dogs. Osteonecrosis was treated with either saline (control) or autologous mesenchymal stem cells (MSCs) transplantation after decompression. Green fluorescent protein (GFP) was used to track the transplanted MSCs, the differentiation of MSCs were evaluated by fluorescent double‐labeling with GFP between osteocalcin or von Willebrand factor (vWF) at 2nd, 8th, and 12th week after the transplantation. It was demonstrated that GFP‐positive cells were present in the necrotic area up to 12 weeks after the transplantation, their number increased from 15% at 2nd week to 38% at 12th week (p < 0.05). Neither osteocalcin nor vWF was detected by immunocytochemistry in GFP‐labeled MSCs in vitro, but osteocalcin was immunohistochemically positive in 90% of the GFP‐labeled MSCs in vivo, while vWF was still negative. The vWF expression was of no significant difference between the control group and MSCs‐transplanted group. The percentages of trabeculae bone volume were 9.36% and 8.42% at 2nd week (p > 0.05), 22.82% and 14.72% at 8th week, and 31.08% and 20.66% at 12th week (p < 0.05) in MSCs‐transplanted group and control group, respectively; new trabeculae bone in MSCs‐transplanted group was significantly increased as compared to that of control group at 8th and 12th week. The results demonstrated that the transplanted MSCs could survive, proliferate, and differentiate into osteoblasts directly, which contributed to the accelerated repair process. The possible mechanism is site‐dependant differentiation. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 27: 442–446, 2009
'Tomudex' (ZD1694): a novel thymidylate synthase inhibitor with clinical antitumour activity in a range of solid tumours. 'Tomudex' International Study Group.

BACKGROUND Anti-metabolites such as methotrexate (MTX) and 5-fluorouracil (5-FU) have been used clinically for many years. Although their effects are partly due to thymidylate synthase (TS) inhibition, they also have non-specific, non TS effects on RNA and purine synthesis. Direct and specific TS inhibitors therefore presented an attractive research target. Collaborative research between the Institute of Cancer Research and Zeneca Pharmaceuticals led to the design of specific folate based quinazoline TS inhibitors. ZD1694 ('Tomudex'), the first of these drugs reaching advanced clinical development, is currently completing phase III studies. DESIGN Eight phase II trials were carried out using 'Tomudex', 3.0 mg/m2, given as a short 15-minute infusion 3-weekly. RESULTS 'Tomudex' demonstrates activity in a range of tumour types, most notably advanced colorectal and breast cancer (objective response rate 26%) and has acceptable toxicity: the most common WHO grade 3 and 4 adverse events were self-limiting reversible increases in liver transaminases, transient leucopenia, diarrhoea, nausea and vomiting and tiredness or malaise. Mucositis/stomatitis, alopecia and skin toxicity were notable for their low incidence and mild intensity. CONCLUSIONS 'Tomudex' represents the successful culmination of a rational drug design programme, and shows promise as a new cytotoxic for the treatment of colorectal cancer. Further studies in other tumour types are planned.
The gammaherpesvirus chemokine binding protein can inhibit the interaction of chemokines with glycosaminoglycans

Chemokines are small glycosaminoglycan (GAG) binding proteins that direct the migration of leukocytes by signaling through G protein coupled receptors (GPCR). Many viruses encode proteins that disrupt chemokine responses. The murine gammaherpesvirus‐68 gene M3 encodes a chemokine binding protein (vCKBP‐3), which has no sequence similarity to chemokine receptors. Initial characterization of vCKBP‐3 showed that it inhibits receptor binding and chemokine‐induced calcium influx. The structural requirements for the chemokines CXCL8 and CCL2 to bind to vCKBP‐3 have been determined. Both chemokines bind to vCKBP‐3 via their N‐loop, a site that can participate in GAG binding for some chemokines. We have investigated the effect of vCKBP‐3 on the interaction of chemokines with GAGs. We found that vCKBP‐3 can prevent a range of chemokines from binding to GAGs. Moreover, we also found that vCKBP‐3 can displace chemokines from a heparin‐coated surface. Together, these data imply that vCKBP‐3 can inhibit chemokine activity at two distinct levels. First, it inhibits chemokines from binding to their GPCR. Second, it inhibits their GAG binding and disrupts pre‐formed chemokine gradients. This dual ability of vCKBP‐3 makes it a more effective inhibitor of chemokine activity.