Miracle-dz/UniFAR-FTUs huggingface dataset:
A Wound‐Isolated Pseudomonas aeruginosa Grows a Biofilm In Vitro Within 10 Hours and Is Visualized by Light Microscopy

BACKGROUND. In chronic wounds, biofilms probably play a vital role in protecting bacteria from host defenses and antimicrobial medications by creating a barrier of exopolysaccharide that is difficult for the immune system and antibiotics to penetrate. A biofilm consists of an exopolysaccharide matrix that is produced and secreted by certain species of bacteria. OBJECTIVE. The purpose of this study was to visualize and time the progressing growth of a biofilm by a wound‐isolated Pseudomonas aeruginosa. METHODS. P. aeruginosa that was initially isolated from a human burn wound was allowed to grow a biofilm in vitro. We used a modified Congo red staining technique to demonstrate the sequential development of a mature biofilm as examined by light microscopy. RESULTS. We show that the exopolysaccharide of the developing biofilm is visible in just 5 hours after inoculation and has the characteristics of a mature biofilm by 10 hours. CONCLUSION. The rapidity of biofilm growth suggests that bacteria in wounds possess the capacity of producing this shield against antibiotics and immune effector cells early in the infection process. Therefore, efforts to prevent or slow the proliferation of bacteria and biofilms should occur soon after a wound is created. Additionally, this staining technique can be used to demonstrate the ability of agents to slow biofilm growth or to interrupt formed biofilm and may be useful in future studies of chronically infected wounds.
Meat, a natural symbol

PART ONE: Background 1. Food=Meat 2. A Brief History of Meat Eating 3. A Matter of Taste 4. More Than a Meal PART TWO: Meat is Muscle 5. Evolution and Elevation 6. The Power of Meat 7. The Barbarity of Meat PART THREE: Mixed Metaphors 8. The Reluctant Cannibal 9. Pets and other Grey Animals 10. The Joy of Sex PART FOUR: Modern Meatologies 11. Economics 12. Health 13. Ethics 14. Ecology 15. Conclusions.
A Potential Causal Association Mining Algorithm for Screening Adverse Drug Reactions in Postmarketing Surveillance

Early detection of unknown adverse drug reactions (ADRs) in postmarketing surveillance saves lives and prevents harmful consequences. We propose a novel data mining approach to signaling potential ADRs from electronic health databases. More specifically, we introduce potential causal association rules (PCARs) to represent the potential causal relationship between a drug and ICD-9 (CDC. (2010). International Classification of Diseases, Ninth Revision (ICD-9). [Online]. Available: http://www.cdc. gov/nchs/icd/icd9.html) coded signs or symptoms representing potential ADRs. Due to the infrequent nature of ADRs, the existing frequency-based data mining methods cannot effectively discover PCARs. We introduce a new interestingness measure, potential causal leverage, to quantify the degree of association of a PCAR. This measure is based on the computational, experience-based fuzzy recognition-primed decision (RPD) model that we developed previously (Y. Ji, R. M. Massanari, J. Ager, J. Yen, R. E. Miller, and H. Ying, “A fuzzy logic-based computational recognition-primed decision model,” Inf. Sci., vol. 177, pp. 4338-4353, 2007) on the basis of the well-known, psychology-originated qualitative RPD model (G. A. Klein, “A recognition-primed decision making model of rapid decision making,” in Decision Making in Action: Models and Methods, 1993, pp. 138-147). The potential causal leverage assesses the strength of the association of a drug-symptom pair given a collection of patient cases. To test our data mining approach, we retrieved electronic medical data for 16 206 patients treated by one or more than eight drugs of our interest at the Veterans Affairs Medical Center in Detroit between 2007 and 2009. We selected enalapril as the target drug for this ADR signal generation study. We used our algorithm to preliminarily evaluate the associations between enalapril and all the ICD-9 codes associated with it. The experimental results indicate that our approach has a potential to better signal potential ADRs than risk ratio and leverage, two traditional frequency-based measures. Among the top 50 signal pairs (i.e., enalapril versus symptoms) ranked by the potential causal-leverage measure, the physicians on the project determined that eight of them probably represent true causal associations.
Linked Tumor-Selective Virus Replication and Transgene Expression from E3-Containing Oncolytic Adenoviruses

ABSTRACT Historically, the adenoviral E3 region was found to be nonessential for viral replication in vitro. In addition, adenoviruses whose genome was more than approximately 105% the size of the native genome were inefficiently packaged. These profound observations were used experimentally to insert transgenes into the adenoviral backbone. More recently, however, the reintroduction of the E3 region into oncolytic adenoviruses has been found to positively influence antitumor efficacy in preclinical models and clinical trials. In the studies reported here, the granulocyte-macrophage colony-stimulating factor (GM-CSF) cDNA sequence has been substituted for the E3-gp19 gene in oncolytic adenoviruses that otherwise retained the E3 region. Five viruses that differed slightly in the method of transgene insertion were generated and compared to Ar6pAE2fGmF (E2F/GM/ΔE3), a previously described E3-deleted oncolytic adenovirus encoding GM-CSF. In all of the viruses, the human E2F-1 promoter regulated E1A expression and GM-CSF expression was under the control of the adenoviral E3 promoter and the packaging signal was relocated immediately upstream from the right terminal repeat. The E3-gp19-deleted viruses had similar cytolytic properties, as measured in vitro by cytotoxicity assays, but differed markedly in their capacity to express and secrete GM-CSF. Ar15pAE2fGmF (E2F/GM/E3b), the virus that produced the highest levels of GM-CSF and retained the native GM-CSF leader sequence, was selected for further analysis. The E2F/GM/E3b and E2F/GM/ΔE3 viruses exhibited similar cytotoxic activity and GM-CSF production in several tumor cell lines in vitro. However, when compared in vivo in nude mouse xenograft tumor models, E2F/GM/E3b spread through tumors to a greater extent, resulted in higher peak GM-CSF and total exposure levels in both tumor and serum, and was more efficacious than the E3-deleted virus. Using the matched WI-38 (parental) and WI-38-VA13 (simian virus 40 large T antigen transformed) cell pair, GM-CSF was shown to be selectively produced in cells expressing high levels of E2F, indicating that the tumor-selective E2F promoter controlled E1A and GM-CSF expression.
Climate Change and Pastoral Economy in Kenya: A Blinking Future

The present paper examines the changing climatic scenarios and associated effects on livestock farming (pastoralism) in the arid and semi arid lands (ASAL) of Kenya, which cover over 80% of the country. The study was carried out in the semi arid Mukogodo Division of Laikipia District in Kenya. This division received a mean annual rainfall of approximately 507.8 mm and the main source of livelihood was pastoralism. Questionnaire, structured interview, observation and literature review were the main methods of data collection. Rainfall was used in delineating changes in climate. Standardized precipitation index (SPI) and Markov process were used in analyzing drought severity and persistence, respectively. Approximately 38% of all droughts between 1975 and 2005 were prolonged and extremely severe, with cumulative severity indices ranging between −2.54 and −6.49. The probability that normal climatic conditions persisted for two or more consecutive years in Mukogodo Division remained constant at approximately 52%. However, the probability of wet years persisting for two or more years showed a declining trend, while persistence of dry years increased with duration. A drying climatic trend was established. This drying trend in the area led to increased land degradation and encroachment of invasive nonpalatable bushes. The net effect on pastoralism was large‐scale livestock loss through starvation, disease and cattle rustling. Proper drought monitoring and accurate forecasts, community participation in all government interventions, infrastructural development in the ASAL and allocation of adequate resources for livestock development are some of the measures necessary for mitigating the dwindling pastoral economy in Kenya and other parts of the world.
Issues of uncertainty in super-resolution mapping and their implications for the design of an inter-comparison study

Super-resolution mapping is a relatively new field in remote sensing whereby classification is undertaken at a finer spatial resolution than that of the input remotely sensed multiple-waveband imagery. A variety of different methods for super-resolution mapping have been proposed, including spatial pixel-swapping, spatial simulated annealing, Hopfield neural networks, feed-forward back-propagation neural networks and geostatistical methods. The accuracy of all of these new approaches has been tested, but the tests have tended to focus on the new technique (i.e. with little benchmarking against other techniques) and have used different measures of accuracy. There is, therefore, a need for greater inter-comparison between the various methods available, and a super-resolution inter-comparison study would be a welcome step towards this goal. This paper describes some of the issues that should be considered in the design of such a study.
Elevated serum C-reactive protein level predicts a poor prognosis for recurrent gastric cancer

Backgrounds High serum C-reactive protein (CRP) was found to be associated with poor prognosis in kinds of solid tumors, however, its role in the recurrent gastric cancer (RGC) is unknown. The present study aimed to explore the prognostic value of serum CRP in RGC patients. Methods A total 72 RGC patients who underwent radical surgery from January 2005 to May 2008 were enrolled. The clinical, pathological and survival information were collected. The serum CRP level was measured when the recurrence was confirmed, and the association between serum CRP and clinicopathological characters was analyzed. The prognostic value of serum CRP for RGC was investigated. Results The serum CRP was elevated in 39 patients (H-CRP), while 33 patients were within the normal range (N-CRP). The elevated CRP was associated with Lymph node metastasis (p = 0.003) and tumor size (p = 0.004). The median survival time after recurrence was significantly worse in the H-CRP group than N-CRP group (6.5 months vs. 11.5 months, p = 0.012). Multivariate analyses identified that elevated CRP level (HR=2.325, p < 0.001), time to recurrence (HR = 0.466, p=0.033), and the follow-up treatment (HR = 2.650, p=0.001) were independent prognostic factors. Conclusions High serum CRP level was associated with aggressive pathological features, was an independent poor prognostic factors for RGC, which might be a potential prognostic marker for RGC patients.
Split ejaculation study: semen parameters and calcium and magnesium in seminal plasma

Objectives Male infertility is on the rise. Artificial insemination is an option in many cases like oligozoospermia or oligoasthenozoospermia. Homologous insemination is helpful for some couples in whom sperm count is low. This study was aimed to understand the most suitable portion of split ejaculate for insemination and also the level of calcium and magnesium in each split. Materials and methods A total number of 31 normal and clinically healthy adults participated in this study. They were instructed to maintain abstinence for 2-5 days prior to sample collection in three splits. Each split was evaluated as if it were a whole sample, following WHO criteria. Seminal plasma was separated. Calcium and magnesium levels were measured in seminal plasma and spermatozoa of each split. Results The split ejaculate study revealed that the first portion contained a higher number of spermatozoa with better motility than the 2nd and 3rd splits. Similarly, the level of calcium and magnesium in seminal plasma and spermatozoa was greater in the first split, followed by 2nd and 3rd splits. Conclusion The presented split ejaculate study has shown the first ejaculate as superior in quality in terms of total sperm count and percentage of active motility. The first split of ejaculation is recommended for homologous artificial insemination in case of oligozoospermia and oligoasthenozoospermia. This study has also shown that a major portion of two important elements, calcium and magnesium, is contributed by the prostate gland.
Statistical Fault Analysis

Statistical Fault Analysis, or Stafan, is proposed as an alternative to fault simulation of digital circuits. This method defines Controllabilities and observabilities of circuit nodes as probabilities estimated from signal statistics of fault-free simulation. Special Procedures deal with these quantities at fanout and feedback nodes. The computed probabilities are used to derive unbiased estimates of fault detection probabilities and overall fault coverage for the given set of input vectors. Among Stafan's advantages, fault coverage and the undetected fault data obtained for actual circuits are shown to agree within five percent of fault simulator results, yet CPU time and memory demands fall far short of those required in fault simulation. The Computational complexity added to a fault-free simulator by Stafan grows only linearly with the number of circuit nodes.
Phylogenetic systematics of chelonioid sea turtles

Abstract Chelonioid sea turtles (Order Testudinata; Superfamily Chelonioidea) first appear in the early Cretaceous (Aptian-Albian). Their long fossil record is excellent compared to most marine tetrapods. Nonetheless, there has been no inclusive attempt to provide an analysis of cladistic relationships among this group. In this paper, the following chelonioid classification is proposed, based on 76 characters among 20 fossil and six living well- represented genera: 1Family Cheloniidae (Coniacian to Recent); Toxochelys, Ctenochelys, Osteopygis, Erquelinnesia, Allopleuron, Argillochelys, Puppigerus, Eochelone, Syllomus, Natator, Eretmochelys, Chelonia, Caretta, Lepidochelys 2Family Protostegidae (Aptian to Maastrichtian? ); ‘Santana new protostegid’,Rhinochelys, Notochelone, Desmatochelys, Chelosphargis, Protostega, Archelon 3Family Dermochelyidae (Santonian? to Recent); Corsochelys, ‘HMG new dermo-chelyid’, Eosphargis, Psephophorus, Dermochelys.
Benthic foraminiferal assemblages from the eastern South Atlantic Polar Front region

Abstract Surface sediment samples taken with a multiple corer from the Polar Front region along two profiles in the eastern South Atlantic sector between 35° and 57°S have been investigated for their benthic foraminiferal content. Live fauna was differentiated from the death assemblage. Based on the dead assemblages, potential fossil assemblages (dead fauna reduced by non-resistant agglutinants) were calculated for comparison with upper Neogene core material. The distribution of the potential fossil assemblages defined byQ-mode principal component analysis mirrors the Recent hydrographic, as well as the trophic situation in the eastern South Atlantic (ocean circulation and productivity). Two Southern Component Bottom Water Faunas reflect the northward flow of Antarctic Bottom Water (AABW) and Lower Circum-Polar Deep Water (LCDW): an assemblage dominated by the arenaceousMultifidella nodulosa below the Calcite Compensation Depth (CCD), and aNuttallides umbonifer dominated assemblage above the CCD. In the region of highest bio-silicious primary productivity, south of the Polar Front and north of the winter sea-ice limit, these faunas are overprinted by a Southern High-productivity Fauna, dominated by infaunal species such asPullenia bulloides,Melonis pompilioides andM. zaandamae. North Atlantic Deep Water (NADW) meets the Circum-Polar Deep Water (CDW) at intermediate depth, as reflected in the distribution of the Northern Component Deep Water Fauna, dominated byEpistominella exigua. The high-productivity assemblage overprinting this fauna, the Northern High-productivity Fauna, is dominated by the shallow endobenthicBulimina aculeata. A Strong Bottom-current Fauna, dominated byAngulogerina angulosa, characterizes areas between 400 and 900 m water depth with sandy sediment, independent from water mass characteristics and food supply.
The integrated approach in Malaysian education: the International Islamic University Malaysia as the model

Reformasi pendidikan di Malaysia pada tahun 1980an dan 1990an mempunyai hubungan rapat dengan saranan-saranan daripada Persidangan Sedunia Mengenai Pendidikan Yang Pertama di Makkah pada tahun 1977 dan juga kesedaran tentang lcepentingan nitai moral dan akhlak. Pendidikan di Malaysia bukan sahaja bagi tujuan pemupukan perpaduan nasional dalam konteks masyarakat herbilang kaum tetapijuga penyepaduan ilmu. Makalah ini menyorot usaha-usaha untuk menjelmakan pendidikan bersepadu dari peringkat sekalah sehingga lcemuncaknya di peringkat pengajian tinggi melalui penubuhan dan peranan Universiti Islam Antarabangsa Malaysia (UlAM). Kejayaan UIAM dari sudut penyepaduan ilmu pengetahuan dan melahirkan pelajar yang holistik telah menjadikan ia model bagi banyak institusi Islam dalam dan luar negara. Perkembangan UlAM dari sudut ilmu-ilmu Islam seperti disiplin ekanomi dan lcewangan Islam yang praktikal dan pengaruhnya melalui pelajar antarabangsa memungkinkan peranannya yang lebih besar Ice arah kebangkitan semula zaman lcegemitangan Islam.
Selected cardiopulmonary values and baroreceptor reflex in conscious green iguanas (Iguana iguana).

OBJECTIVE To determine selected cardiopulmonary values and baroreceptor response in conscious green iguanas (Iguana iguana) and to evaluate the use of blood gas analysis and pulse oximetry in this species. ANIMALS 15 healthy juvenile green iguanas. PROCEDURES Baseline cardiopulmonary values were determined in 15 conscious iguanas breathing room air. Effects of 100% O(2) inspiration were also measured (n = 6), and the baroreceptor reflex was characterized by exponential sigmoidal curve fitting analysis. RESULTS Conscious iguanas had a mean ± SD resting heart rate of 52 ± 8 beats/min, respiratory rate of 28 ± 6 breaths/min, and systolic, mean, and diastolic arterial blood pressures of 69 ± 10 mm Hg, 62 ± 12 mm Hg, and 56 ± 13 mm Hg, respectively. Mean arterial pH at 37°C was 7.29 ± 0.11, PaO(2) was 81 ± 10 mm Hg, and PaCO(2) was 42 ± 9 mm Hg; corrected for a body temperature of 30°C, mean arterial pH at 37°C was 7.382 ±0.12, PaO(2) was 54 ± 15 mm Hg, and PaCO(2) was 32 ± 7 mm Hg. Inspiration of 100% O(2) did not change heart and respiratory rates but increased PaO(2) to 486 ± 105 mm Hg (corrected value, 437 ± 96 mm Hg). A baroreceptor reflex was evident, with mean heart rates ranging from 30 ± 3 beats/min to 63 ± 5 beats/min and mean arterial blood pressures ranging from 42 ± 3 mm Hg to 58 ± 3 mm Hg. CONCLUSIONS AND CLINICAL RELEVANCE This study provided needed information on cardiopulmonary values in healthy green iguanas, the application and limitation of arterial and venous blood gas analysis, and the accuracy of pulse oximetry.
Role of the Southern Annular Mode (SAM) in Southern Ocean CO2 uptake

A biogeochemical ocean general circulation model, driven with NCEP‐R1 and observed atmospheric CO2 history, is used to investigate and quantify the role that the Southern Annular Mode (SAM), identified as the leading mode of climate variability, has in driving interannual variability in Southern Ocean air‐sea CO2 fluxes between 1980 and 2000. Our simulations show the Southern Ocean to be a region of decreased CO2 uptake during the positive SAM phase. The SAM induces changes in Southern Ocean CO2 uptake with a 2‐month time lag explaining 42% of the variance in the total interannual variability in air‐sea CO2 fluxes. Our analysis shows that the response of the Southern Ocean to the SAM is primarily governed by changes in ΔpCO2 (67%), and that this response is driven by changes in ocean physics that control the supply of nutrients to the upper ocean, primarily Dissolved Inorganic Carbon (DIC). The SAM is predicted to become stronger and more positive in response to climate change and our results suggest this will decrease the Southern Ocean CO2 uptake by 0.1PgC/yr per unit change in the SAM.
Anaerobic methanotrophic community of a 5346-m-deep vesicomyid clam colony in the Japan Trench

Vesicomyidae clams harbor sulfide‐oxidizing endosymbionts and are typical members of cold seep communities where active venting of fluids and gases takes place. We investigated the central biogeochemical processes that supported a vesicomyid clam colony as part of a locally restricted seep community in the Japan Trench at 5346 m water depth, one of the deepest seep settings studied to date. An integrated approach of biogeochemical and molecular ecological techniques was used combining in situ and ex situ measurements. In sediment of the clam colony, low sulfate reduction rates (maximum 128 nmol mL−1 day−1) were coupled to the anaerobic oxidation of methane. They were observed over a depth range of 15 cm, caused by active transport of sulfate due to bioturbation of the vesicomyid clams. A distinct separation between the seep and the surrounding seafloor was shown by steep horizontal geochemical gradients and pronounced microbial community shifts. The sediment below the clam colony was dominated by anaerobic methanotrophic archaea (ANME‐2c) and sulfate‐reducing Desulfobulbaceae (SEEP‐SRB‐3, SEEP‐SRB‐4). Aerobic methanotrophic bacteria were not detected in the sediment, and the oxidation of sulfide seemed to be carried out chemolithoautotrophically by Sulfurovum species. Thus, major redox processes were mediated by distinct subgroups of seep‐related microorganisms that might have been selected by this specific abyssal seep environment. Fluid flow and microbial activity were low but sufficient to support the clam community over decades and to build up high biomasses. Hence, the clams and their microbial communities adapted successfully to a low‐energy regime and may represent widespread chemosynthetic communities in the Japan Trench. In this regard, they contributed to the restricted deep‐sea trench biodiversity as well as to the organic carbon availability, also for non‐seep organisms, in such oligotrophic benthic environment of the dark deep ocean.
ATP P2X Receptor-Mediated Enhancement of Glutamate Release and Evoked EPSCs in Dorsal Horn Neurons of the Rat Spinal Cord

Presynaptic ATP P2X receptors have been proposed to play a role in modulating glutamate release from the first sensory synapse in the spinal cord. Using spinal cord slice preparations and patch-clamp recordings from dorsal horn neurons in lamina V of the rat spinal cord, we showed that the activation of P2X receptors by α,β-methylene-ATP (αβm-ATP) resulted in a large increase in the frequency of spontaneous EPSCs (sEPSCs) and miniature EPSCs (mEPSCs). The increases in mEPSC frequency by αβm-ATP were not blocked by the Ca2+ channel blocker, 30 μmLa3+, but were abolished in a bath solution when Ca2+ was omitted. The increases in mEPSC frequency by αβm-ATP were blocked completely by the P2 receptor antagonist pyridoxalphosphate-6-azophenyl-2′,4′-disulfonic acid (PPADS) at 10 μm. Furthermore, the EPSCs evoked by dorsal root stimulation were potentiated by αβm-ATP as well as by the ecto-ATPase inhibitor ARL67156 and were depressed in the presence of P2 receptor antagonists PPADS (10 μm) and suramin (5 μm). The effects of these compounds on the evoked EPSCs were associated with the changes in glutamate release probability of primary afferent central terminals. Our results indicate that αβm-ATP-sensitive P2X receptors play a significant role in modulating excitatory sensory synaptic transmission in the spinal cord, and the potential role of endogenous ATP is suggested.