Miracle-dz/UniFAR-FTUs huggingface dataset:
Extraction, Purification and Characterization of Lipopolysaccharide from Escherichia coli and Salmonella typhi

Lipopolysaccharide (LPS) is an important structural component of the outer cell membrane complex of gram negative microorganisms. Its causative role in gram negative bacteria-induced diseases and broad applications in different kinds of cell stimulation experiments provided a conceptual basis for studies directed at the isolation, purification, and detailed chemical characterization of LPS. The main problem with LPS purification protocols is the contamination of the end product with nucleic acids and proteins in variable proportions which could potentially interfere with downstream applications. In this study, a simple procedure for purification of LPS from Escherichia coli (E.coli) and Salmonella typhi (S.typhi) with high purity and very low contaminating nucleic acids and proteins based on the hot phenol-water extraction protocol has been introduced. The purity of extracted LPS was evaluated by silver and coomassie blue staining of SDS-PAGE gels and HPLC analysis. Limulus Amebocyte Lysate (LAL) coagulation activity and rabbit pyrogen assay were exploited to monitor the functionality of purified LPS. The results showed that DNase and RNase treatment of the sample is essential after the sonication step to eliminate nucleic acid contamination in the LPS fraction. Silver staining demonstrated ladder pattern which is characteristic of LPS. No contaminating protein was found as assessed by coomassie blue staining. HPLC fractionation revealed high degree of purity comparable with commercial LPS. Parenteral administration of purified LPS resulted in substantial increase of rabbits’ body temperature (mean: 1.45°C). LAL coagulation assay confirmed the functional activity of the purified LPS. In conclusion, the protocol presented here could be employed for isolation of LPS with high purity and functional activity.
Causes of East Asian Temperature Multidecadal Variability Since 850 CE

The drivers of multidecadal‐ to centennial‐scale variability in East Asian temperature, apparent in temperature reconstructions, are poorly understood. Here we apply a multivariate regression analysis to distinguish the influences of large‐scale modes of internal variability (Atlantic Multidecadal Oscillation and Pacific Multidecadal Oscillation) and external natural (orbital, solar, and volcanic) and anthropogenic (greenhouse gas concentrations, aerosols, and land use changes) forcings on East Asian warm‐season temperature over the period 850–1999 CE (Common Era). We find that ~80% of the temperature change on time scales longer than 30 years can be explained including all drivers over the full‐length period. The Pacific Multidecadal Oscillation was the most important driver of multidecadal temperature variability during the Medieval Climate Anomaly (here 950–1250), while solar contribution was important during the Little Ice Age (here 1350–1850). Since 1850, two thirds of temperature change can be explained with anthropogenic forcing, whereas one third was related mainly to the Atlantic Multidecadal Oscillation and volcanic forcing.
Possible Usefulness of Gadolinium-Enhanced Brain MRI for Evaluating Risk of Perioperative Hemorrhage: A Case of Infective Endocarditis

A 59-year-old woman visited a local hospital for fever and was diagnosed as having infective endocarditis (IE) on the basis of blood cultures and transthoracic echocardiography. Based on clinical episodes of subarachnoid hemorrhage after admission, it was judged that she was not a good candidate for urgent open heart surgery, and it was decided to treat her with conservative medical therapy for the acute phase. We explored the optimum timing for surgery by employing gadolinium (Gd) contrast medium-enhanced magnetic resonance imaging (MRI) T2* weighted image (black dots) due to her high risk of perioperative cerebral hemorrhage. After the disappearance of the contrast media enhancement effect around the black dots, open heart surgery was performed successfully on the 103rd hospitalization day. The patient was discharged 22 days after the surgery with no clinical complications. This case suggests that disappearance of the contrast media enhancement effect around the black dots may be a useful marker for optimal timing of surgery to minimize the risk of perioperative cerebral hemorrhage in patients with IE. Learning Objective. The MRI T2* weighted images including those with Gd contrast medium enhancement effect may be useful for evaluating the risk of perioperative intracranial hemorrhage in IE.
Patients' preferences for adjuvant chemotherapy in early-stage breast cancer: is treatment worthwhile?

When making decisions about adjuvant chemotherapy for early-stage breast cancer, costs and benefits of treatment should be carefully weighed. In this process, patients’ preferences are of major importance. The objectives of the present study were: (1) to determine the minimum benefits that patients need to find chemotherapy acceptable, and (2) to explore potential preference determinants, namely: positive experience of the treatment, reconciliation with the treatment decision, and demographic variables. Preferences were elicited from patients scheduled for adjuvant chemotherapy (chemotherapy group: n = 38) before (T1), during (T2), and 1 month after chemotherapy (T3), and were compared to responses from patients not scheduled for chemotherapy (no-chemotherapy group: n = 38). The patients were asked, for a hypothetical situation, to indicate the minimum benefit (in terms of improved 5-year disease-free survival) to find adjuvant chemotherapy acceptable. In the chemotherapy group, the median benefit was 1% at all 3 measurement points. In the no-chemotherapy group the attitude towards chemotherapy became more negative over time, although not statistically significantly so (T1: 12%, T2: 15%, T3: 15%;P = 0.10). At all measurement points, the patients in the chemotherapy group indicated that they would accept chemotherapy for significantly (P< 0.01) less benefit than the patients in the no-chemotherapy group. Of the demographic variables, age was related to preferences, but only at T2and only in the no-chemotherapy group. The more positive attitude towards chemotherapy and the stability of preferences in the chemotherapy group indicated that reconciliation with the treatment decision was a more important determinant of patients’ preferences than positive experience of the treatment. © 2001 Cancer Research Campaign http://www.bjcancer. com
Oxidant‐antioxidant status in relation to survival among breast cancer patients

The role of plasma oxidant‐antioxidant status in survival after breast cancer surgery was investigated in a cohort of patients (n = 363) hospitalized in Southern France between 1989 and 1992. The median follow‐up was 8 years after surgery for histologically confirmed breast cancer. Plasma analyses were performed after diagnosis and before surgery and adjuvant therapy. We found an inverse relationship between plasma lipoperoxides (MDA) and tumor size at diagnosis, together with higher lipoperoxide levels in node‐negative tumors than in node‐positive ones (TNM). The longitudinal approach revealed an increased risk of recurrence for patients with plasma lipoperoxides in the highest tertile of the sample (RR = 2.1, 95%CI 1.1–4.0). In addition, the risk of recurrence increased (RR = 1.7, 95%CI 1.0–3.0), after adjustment for the known prognostic factors (TNM), for patients with plasma lipid‐adjusted vitamin E levels of over 22 μmol/l. The risk of breast cancer death was twice as great for patients with plasma lipid‐adjusted vitamin E levels above this value. Excesses of plasma lipoperoxides and vitamin E appear to be factors in poor prognosis for breast cancer‐specific survival (OVS) and disease‐free survival (DFS), respectively, independent of tumor characteristics at diagnosis. Several hypotheses are advanced to explain the possible role of plasma vitamin E as a factor in poor prognosis for survival. © 2001 Wiley‐Liss, Inc.
Microorganisms in the aetiology of atherosclerosis

Recent publications have suggested that infective pathogens might play an important role in the pathogenesis of atherosclerosis. This review focuses on these microorganisms in the process of atherosclerosis. The results of in vitro studies, animal studies, tissue studies, and serological studies will be summarised, followed by an overall conclusion concerning the strength of the association of the microorganism with the pathogenesis of atherosclerosis. The role of the bacteria Chlamydia pneumoniae and Helicobacter pylori, and the viruses human immunodeficiency virus, coxsackie B virus, cytomegalovirus, Epstein-Barr virus, herpes simplex virus, and measles virus will be discussed.
Biological characteristics of CD133+ cells in nasopharyngeal carcinoma

Cancer stem cells are regarded as the cause of tumour formation and recurrence in nasopharyngeal carcinoma (NPC). However, ideal surface markers for stem cells in NPC remain unidentified. In the present study, we investigated the expression of CD133, Nanog and Sox2 in the nasopharyngeal carcinoma cell line CNE2 and primarily cultured NPC cells using immunofluorescence or flow cytometry. A cell population with a CD133+ phenotype was enriched using magnetic-activated cell sorting technology. We demonstrated that CD133+ cells exhibited a strong potential for self-renewal, proliferation and differentiation and a greater potential for in vivo tumour formation in nude mice compared to CD133− cells, although the percentage of CD133+ cells was small. However, the specific marker antigens Nanog and Sox2 were simultaneously expressed in normal cancer stem cells. Our results showed that CD133 can serve as a specific surface marker for nasopharyngeal cancer stem cells.
Irrigation efficiency and water-policy implications for river basin resilience

Rising demand for food, fiber, and biofuels drives expanding irrigation withdrawals from surface water and groundwater. Irrigation efficiency and water savings have become watchwords in response to climate-induced hydrological variability, increasing freshwater demand for other uses including ecosystem water needs, and low economic productivity of irrigation compared to most other uses. We identify three classes of unintended consequences, presented here as paradoxes. Ever-tighter cycling of water has been shown to increase resource use, an example of the efficiency paradox . In the absence of effective policy to constrain irrigated-area expansion using "saved water", efficiency can aggravate scarcity, deteriorate resource quality, and impair river basin resilience through loss of flexibility and redundancy. Water scarcity and salinity effects in the lower reaches of basins (symptomatic of the scale paradox ) may partly be offset over the short-term through groundwater pumping or increasing surface water storage capacity. However, declining ecological flows and increasing salinity have important implications for riparian and estuarine ecosystems and for non-irrigation human uses of water including urban supply and energy generation, examples of the sectoral paradox . This paper briefly considers three regional contexts with broadly similar climatic and water-resource conditions – central Chile, southwestern US, and south-central Spain – where irrigation efficiency directly influences basin resilience. The comparison leads to more generic insights on water policy in relation to irrigation efficiency and emerging or overdue needs for environmental protection.
N-methyl-d-aspartate Receptor Antagonist Ketamine Impairs Action-monitoring Activity in the Prefrontal Cortex

Failures in monitoring of self-generated actions are thought to underlie the positive symptoms in schizophrenia. It has been hypothesized that these deficits may be caused by a dysfunction of N-methyl-d-aspartate receptors (NMDARs). Here we recorded the activity of prefrontal neurons in monkeys performing an antisaccade task, while we administered a subanesthetic dose of the noncompetitive NMDAR antagonist ketamine. Many neurons discriminated between correct antisaccades and response errors in their postresponse activity. Ketamine increased the activity for the neurons' nonpreferred response, thereby decreasing the neurons' performance selectivity. Ketamine also affected the monkeys' behavior after an error, consistent with a deficit in error detection. The results show that NMDARs play an important role in action monitoring in primates. The decrease in performance selectivity of prefrontal neurons after ketamine can help to explain the deficits in action monitoring found in humans after ketamine administration and provides support for the hypothesis that an NMDAR dysfunction underlies self-monitoring deficits and psychotic symptoms in schizophrenia.
Structure and Stability of the Spinach Aquaporin SoPIP2;1 in Detergent Micelles and Lipid Membranes

Background SoPIP2;1 constitutes one of the major integral proteins in spinach leaf plasma membranes and belongs to the aquaporin family. SoPIP2;1 is a highly permeable and selective water channel that has been successfully overexpressed and purified with high yields. In order to optimize reconstitution of the purified protein into biomimetic systems, we have here for the first time characterized the structural stability of SoPIP2;1. Methodology/Principal Finding We have characterized the protein structural stability after purification and after reconstitution into detergent micelles and proteoliposomes using circular dichroism and fluorescence spectroscopy techniques. The structure of SoPIP2;1 was analyzed either with the protein solubilized with octyl-β-D-glucopyranoside (OG) or reconstituted into lipid membranes formed by E. coli lipids, diphytanoylphosphatidylcholine (DPhPC), or reconstituted into lipid membranes formed from mixtures of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPE), 1-palmitoyl-2oleoyl-phosphatidylethanolamine (POPE), 1-palmitoyl-2-oleoyl-phosphatidylserine (POPS), and ergosterol. Generally, SoPIP2;1 secondary structure was found to be predominantly α-helical in accordance with crystallographic data. The protein has a high thermal structural stability in detergent solutions, with an irreversible thermal unfolding occurring at a melting temperature of 58°C. Incorporation of the protein into lipid membranes increases the structural stability as evidenced by an increased melting temperature of up to 70°C. Conclusion/Significance The results of this study provide insights into SoPIP2;1 stability in various host membranes and suggest suitable choices of detergent and lipid composition for reconstitution of SoPIP2;1 into biomimetic membranes for biotechnological applications.
Biofeedback treatment for asthma.

STUDY OBJECTIVES We evaluated the effectiveness of heart rate variability (HRV) biofeedback as a complementary treatment for asthma. PATIENTS Ninety-four adult outpatient paid volunteers with asthma. SETTING The psychophysiology laboratory at The University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, and the private outpatient offices of participating asthma physicians. INTERVENTIONS The interventions were as follows: (1) a full protocol (ie, HRV biofeedback and abdominal breathing through pursed lips and prolonged exhalation); (2) HRV biofeedback alone; (3) placebo EEG biofeedback; and (4) a waiting list control. DESIGN Subjects were first prestabilized using controller medication and then were randomly assigned to experimental groups. Medication was titrated biweekly by blinded asthma specialists according to a protocol based on National Heart, Lung, and Blood Institute guidelines, according to symptoms, spirometry, and home peak flows. MEASUREMENTS Subjects recorded daily asthma symptoms and twice-daily peak expiratory flows. Spirometry was performed before and after each weekly treatment session under the HRV and placebo biofeedback conditions, and at triweekly assessment sessions under the waiting list condition. Oscillation resistance was measured approximately triweekly. RESULTS Compared with the two control groups, subjects in both of the two HRV biofeedback groups were prescribed less medication, with minimal differences between the two active treatments. Improvements averaged one full level of asthma severity. Measures from forced oscillation pneumography similarly showed improvement in pulmonary function. A placebo effect influenced an improvement in asthma symptoms, but not in pulmonary function. Groups did not differ in the occurrence of severe asthma flares. CONCLUSIONS The results suggest that HRV biofeedback may prove to be a useful adjunct to asthma treatment and may help to reduce dependence on steroid medications. Further evaluation of this method is warranted.
Race, gender, and self-presentation in teen profile photographs

This study analyzes how teens represent themselves through their profile photographs on a popular nonymous chat site. Using visual content analysis methods, we analyzed 400 profile photographs, controlling for the self-reported gender and the apparent race of the photographic subject. The analysis finds significant differences in gaze, posture, dress, and distance from the camera according to gender and race, although racial differences are stronger for boys than for girls. To a surprising extent, the findings mirror previous findings of gender and race differences in face-to-face interaction, suggesting that the teens construe their profile images as invitations to interact with others online. At the same time, their photo choices reproduce culturally dominant ideologies of gender and race as reinforced by mass media images.
Do budget-holding physicians respond to price? The case of fundholding in the UK

In an effort to improve the efficiency of the healthcare sector, some countries have experimented with various forms of 'internal market' in public healthcare provision. In some models, policymakers have assumed that actors will behave, as in a retail market, by responding to price in the course of seeking the best 'value for money' from healthcare providers. In the study reported here we examined the responsiveness of general practitioners to price during the British experiment in general practice (GP) fundholding. The study analysed routine data on 29 423 referrals for elective care made by 129 practices in one city to two competing providers of secondary care. Indices of price responsiveness were calculated for each practice from their manifest referral behaviour. These were then used to compare fundholding and non-fundholding practices. The results showed no difference between these groups in their propensity to respond to published procedure prices, even when potential savings were very large. Our findings are consistent with the reported views of fundholding GPs that price was a secondary consideration in their referral behaviour, and provides further evidence that healthcare markets cannot be understood in simplistic terms.
Poor Cell Survival Limits the Beneficial Impact of Mesenchymal Stem Cell Transplantation on Acute Kidney Injury

Background: Although renal tubular epithelium has a great capacity for repair it has been suggested that the administration of mesenchymal stem cells may accelerate the recovery following severe ischemic injury. Methods: Here we analyzed the survival rate and organ distribution of transplanted mesenchymal stem cells as well as their contribution to kidney regeneration after ischemic renal injury using functional tests, histological examination as well as quantitative real-time PCR. Results: Intravenously injected stem cells were mainly trapped in lungs and liver. One hour after injection, less than 1% of the injected stem cells could be detected in the injured kidneys. These cells disappeared within the first few days and did not replace renal epithelial cells precluding substantial transdifferentiation. To clarify whether reinforced stem cell delivery might promote sustained survival or conversion to tubular epithelia, stem cells were directly injected into the injured kidneys. Although these grafted cells also did not show sustained survival or contribute to structural renal repair, stem cell injection was associated with a significant but transient initial decrease in serum creatinine. Conclusion: These data suggest that mesenchymal stem cells do not significantly contribute to epithelial renewal after ischemic injury, promoting the idea that the major impact of cell-based therapy for acute kidney injury may result from paracrine or endocrine effects unrelated to stem cell transdifferentiation.
Practical Aspects of Multi-stage Programming

High-level languages offer abstraction mechanisms that can reduce development time and improve software quality. But abstraction mechanisms often have an accumulative runtime overhead that can discourage their use. Multi-stage programming (MSP) languages offer constructs that make it possible to use abstraction mechanisms without paying a runtime overhead. This paper studies applying MSP to implementing dynamic programming (DP) problems. The study reveals that staging high-level implementations of DP algorithms naturally leads to a code explosion problem. In addition, it is common that high-level languages are not designed to deliver the kind of performance that is desirable in implementations of such algorithms. The paper proposes a solution to each of these two problems. Staged memoization is used for code explosion, and a kind of “offshoring” translation is used to address the second. For basic DP problems, the performance of the resulting specialized C implementations is almost always better than the hand-written generic C implementations.
Unified digital sliding mode control with inductor current ripple reconstruction for DC-DC converters

In this paper, a digital implementation of a unified sliding mode controller for DC-DC converters is presented. Although current information is used as a control variable, a pure voltage-mode implementation has been considered and the inductor current ripple is digitally reconstructed. The proposed universal control algorithm can be applied to different converter topologies and operating modes. In particular, experimental results are shown for a prototyping system of a Buck converter operating in Continuous Conduction Mode (CCM) and Discontinuous Conduction Mode (DCM), where only negligible transient effects are present when changing the operation mode. The presented measurements confirm that the proposed universal control algorithm is capable of achieving tight voltage regulation and excellent dynamic performance under different operating conditions. Additionally, a comparison to a state-of-the-art digital Proportional-Integral-Derivative (PID) controller illustrates the performance improvement of the proposed digital control scheme.
Orientation of the HAARP ELF ionospheric dipole and the auroral electrojet

The HF heating facility of the High Frequency Active Auroral Research Program (HAARP), located near Gakona, Alaska, generates ELF (300 Hz ‐ 3 kHz) waves via modulated HF (2.7–10 MHz) heating of the auroral electrojet. Using two ELF/VLF receivers at ∼700 km from HAARP, the orientation of the equivalent ELF radiating ionospheric dipole is inferred from the relative strength and Earth‐ionosphere waveguide modal content of signals received. In several cases analyzed the effective HAARP electric dipole orientation is generally along magnetic east‐west direction. A new metric is introduced to evaluate the validity of the determination of source characteristics with medium and long‐range ELF/VLF measurements. Results are put into context of the auroral electrojet, indicating the possibility of studying small‐scale electrojet structure not observable with magnetometers.