Microwave (MW) remediation of hydrocarbon contaminated soil using spent graphite - An approach for waste as a resource.

In this study, we have explored the possibility of using an industrial waste for remediation of heavy fuel oil contaminated soil. Microwave (MW) heating in the presence of spent graphite (SG) from an auto forging industry has been used for the remediation. The physico-chemical characterization of SG and contaminated soil were done. Microwave remediation experiments were conducted in a lab scale unit and the effect of different parameters like microwave power, susceptor loading and treatment time were studied and optimized. The contaminated and decontaminated soils were analysed using GC-MS for total petroleum hydrocarbons (TPH), Total Organic Carbon and CHNS analyzers. Batch experiments of soil remediation showed that the TPH removal efficiencies (%) of 41.25, 87.77 and 91.18 at 300, 450 and 600 W respectively at SG concentration of 2.5 (wt. %) for a reaction time of 60 min. The addition of SG as susceptor enhanced the desorption of long chain hydrocarbons (C12-C29) present in the soil. Desorption of hydrocarbons from the soil fits well with first order kinetic model. This study successfully demonstrated the reuse of spent graphite (a lubricant waste) recovered from metal forging operations for remediating the fuel oil contaminated soil.

Clinical profile and risk factors associated with severe scrub typhus infection among non-ICU patients in semi-urban south India.

BACKGROUND & OBJECTIVES: Scrub typhus is as an emerging infectious disease that generally causes acute febrile illness, with disease spectrum ranging from mild illness to multiorgan dysfunction. This study was aimed to report the clinical profile, complications and risk factors associated with severe illness in patients with scrub typhus, outside the intensive care setting. METHODS: It was a prospective study, which involved recruitment of patients with acute febrile illness and diagnosed to have scrub typhus, who were admitted to the general medical wards of a tertiary care centre in Kanchipuram district, in semi-urban south India, over a 12 month period between June 2015 and May 2016. The diagnosis was established both clinically (with or without pathognomonic eschar) and by a positive test of IgM antibodies against scrub typhus by ELISA. The severity of scrub typhus was determined by the presence of organ dysfunction, and the factors associated with it were analyzed. RESULTS: A total of 50 patients with mean age of 39.6±20.5 yr (mean ± SD) were admitted. The mean duration of illness before presentation was 9.10 ± 8.6 days. The mean duration of hospital stay was 7.7±3.6 days. The symptoms included fever, abdominal symptoms, headache, dysuria, breathlessness and altered sensorium. Most common findings on physical examination were eschar (58%), crepitations in the chest (36%), hepatomegaly (34%) and lymphadenopathy (30%). Thirty two percent had respiratory complications, 4% required mechanical ventilation, 24% had shock, 16% had acute kidney injury, and 6% had dysfunction of ≥2 organs. Age of >50 yr, longer duration of illness (>7 days), residence in a rural area and the absence of eschar were found to be independent risk factors for development of severe illness. INTERPRETATION & CONCLUSION: Severe scrub typhus infection among non-ICU patients is more likely to occur in elderly patients and in those with longer duration of illness prior to presentation. The subset of patients without eschar might be more prone to develop complications.

HAM-D17 and HAM-D6 sensitivity to change in relation to desvenlafaxine dose and baseline depression severity in major depressive disorder.

INTRODUCTION: This retrospective analysis compared sensitivity to change on the 17-item and 6-item Hamilton Rating Scales For Depression (HAM-D (17) and HAM-D (6), respectively) in relation to antidepressant dose and baseline depression severity. METHODS: Data were derived from 6 randomized, double-blind, placebo-controlled, 8-week trials of fixed-dose desvenlafaxine (50, 100, 200 or 400 mg/d) for major depressive disorder. HAM-D (17) and HAM-D (6) effect sizes were assessed. RESULTS: HAM-D (17) effect sizes were negative (favoured placebo) for higher desvenlafaxine doses (200-400 mg/d) at week 1, but were positive for all doses after week 2, with no clear dose-response pattern. However, HAM-D (6) effect sizes were positive for all doses at all weeks. Effect sizes were consistently greater for HAM-D (6) vs. HAM-D (17), regardless of time spent under therapy. Effect sizes were greater for HAM-D (6) vs. HAM-D (17) for all desvenlafaxine doses among patients with baseline HAM-D (17) <25, but not among patients with baseline HAM-D (17) ≥ 25. DISCUSSION: The HAM-D (6) demonstrated greater sensitivity to change and robustness than the HAM-D (17), supporting the greater homogeneity of the HAM-D (6).

Impact of various foot arches on dynamic balance and speed performance in collegiate short distance runners: A cross-sectional comparative study.

OBJECTIVE: To compare the impact of foot arches on dynamic balance and speed performance. MATERIALS AND METHODS: 30 collegiate male short distance runners were divided into three groups based on foot arches, high, neutral and low. Balance and speed performance were estimated based on scores of star excursion balance test (SEBT), 40 yard dash test and vertical jump test (VJT). RESULTS: Significant improved scores (p < 0.001) were noted in SEBT, 40 yard dash test and VJT. CONCLUSION: Short distance runners with high arch foot have improved dynamic balance and speed when compared to low and neutral arch foot.

Structure of human des(1-45) factor Xa at 2.2 A resolution.

The structure of a large molecular fragment of factor Xa that lacks only a Gla (gamma-carboxyglutamic acid) domain (N-terminal 45 residues) has been solved by X-ray crystallography and refined at 2.2 A resolution to a crystallographic R-value of 0.168. The fragment identity was clearly established by automated Edman degradation. X-ray structure analysis confirmed the biochemical characterization and also revealed that the N-terminal epidermal growth factor (EGF)-like domain is flexibly disordered in crystals. The second EGF module, however, is positionally ordered making contacts with the catalytic domain. The overall folding of the catalytic domain is similar to that of alpha-thrombin, excluding the insertion loops of the latter with respect to simpler serine proteinases. The C-terminal arginine of the A-chain interacts in a substrate-like manner with the S1 specificity site of the active site of a crystallographically neighboring molecule. Based on this interaction and the structure of D-PheProArg methylene-thrombin, a model of the commonly used dansylGluGlyArg methylene inhibitor-factor Xa interaction is proposed. The region of factor Xa corresponding to the fibrinogen recognition site of thrombin has a reversed electrical polarity to the anion binding fibrinogen recognition site of thrombin but possesses a site similar to the Ca2+ binding site of trypsin and other serine proteinases. The structure of the C-terminal EGF domain of factor Xa is the first to be determined crystallographically. Its folding has been comprehensively compared with similar domains determined by NMR. Although the A-chain makes 44 contacts at less than 3.5 A with the catalytic domain, only 16 involve the EGF module. In addition, the A-chain makes 30 intermolecular contacts with a neighboring catalytic domain.

Structural basis for bending of organic crystals.

Bending is observed in organic crystals when the packing is anisotropic in such a way that strong and weak interaction patterns occur in nearly perpendicular directions.

Compliance with infection control practices in sputum microscopy centres: a study from Kerala, India.

BACKGROUND: One of the strategies of the Revised National Tuberculosis Control Programme in India to achieve tuberculosis control is by increasing case detection through a nationwide network of designated microscopy centres (DMC). Practice of standard precautions for infection control in these DMCs is very important to prevent transmission of infection not only to the laboratory personnel, but also to the general population. However, in India this has not been evaluated by an external agency. METHOD: A cross-sectional study was carried out to assess knowledge, facilities and compliance regarding infection control practices (ICP) in all 38 DMCs in Kannur district, Kerala, India, in 2015. Using observations and interviews, the investigators collected data in a structured format. RESULTS: Overall knowledge about infection control was found to be satisfactory among 29% of laboratory technicians. Overall facilities for infection control were satisfactory in 61% of the DMCs, while adherence to ICP was satisfactory in 45% of the DMCs. Knowledge regarding ICP was better in government DMCs, whereas facilities for ICP and adherence to biomedical waste management guidelines were better in private DMCs. CONCLUSION: Given the higher risk of infection among laboratory technicians, there is an urgent need to address the shortcomings in infection control practices.

Contexte : Une des stratégies du Programme national révisé de lutte contre la tuberculose (RNTCP) en Inde consiste à lutter contre la tuberculose en augmentant la détection des cas à travers un réseau national de Centres de Diagnostic par Microscopie (DMC). La mise en oeuvre des précautions standard de lutte contre les infections dans ces DMC est très importante pour prévenir la transmission des infections, non seulement vis-à-vis du personnel de laboratoire, mais également vis-à-vis de la population générale. Cependant, en Inde, ceci n'a pas été évalué par une agence externe.Méthode : Une étude transversale a été réalisée pour évaluer les connaissances, la structure et l'adhésion aux pratiques de lutte contre l'infection (ICP) dans les 38 DMC du district de Kannur, état du Kerala, Inde en 2015. Grâce à des observations et à des entretiens, les investigateurs ont recueilli des données dans un format structuré.Résultats : Les connaissances d'ensemble relatives à la lutte contre l'infection ont été jugées satisfaisantes pour 29% des techniciens de laboratoire. Le niveau d'ensemble des centres en matière de lutte contre l'infection a été satisfaisant dans 61% des DMC. L'adhésion aux pratiques de lutte contre l'infection a été satisfaisante dans 45% des DMC. Les connaissances relatives aux pratiques d'ICP ont été meilleures dans les DMC du gouvernement tandis que les installations et l'adhésion aux directives de gestion des déchets biomédicaux ont été meilleures dans les DMC privés.Conclusion : Connaissant le risque très élevé d'infection parmi les techniciens de laboratoire, il y a un besoin urgent de corriger les déficiences des pratiques de lutte contre l'infection.

Marco de referencia: Una de las estrategias del Programa Nacional Revisado contra la Tuberculosis de la India consiste en controlar la enfermedad al aumentar la detección de casos por conducto de una red nacional de centros de microscopia diagnóstica (DMC). La práctica de las precauciones corrientes de control de las infecciones en estos centros es muy importante con el fin de evitar la transmisión no solo al personal de laboratorio, sino también a la población general. Sin embargo, ningún organismo externo ha evaluado estas prácticas en el país.Método: Se llevó a cabo un estudio transversal con el fin de evaluar los conocimientos, la adecuación de los establecimientos y el cumplimiento de las prácticas en materia de control de las infecciones (ICP) en 38 DMC del distrito de Kannur en el estado de Kerala en la India en 2015. Los investigadores recogieron datos mediante observaciones y entrevistas estructuradas.Resultados: En general, el 29% del personal auxiliar de laboratorio poseía un grado satisfactorio de conocimientos sobre el control de las infecciones; el 61% de los DMC contaba con dispositivos adecuados de ICP y en el 45% se observó el cumplimiento de las normas. El conocimiento de las ICP fue mayor en los DMC del sector público, pero los dispositivos de los establecimientos y el cumplimiento de las directrices de eliminación de los desechos biológicos fueron de mejor calidad en los DMC del sector privado.Conclusión: Teniendo en cuenta el mayor riesgo de exposición a las infecciones que presenta el personal auxiliar de laboratorio, existe una necesidad urgente de abordar las deficiencias observadas en las prácticas de control de las infecciones.

Structure of tick anticoagulant peptide at 1.6 A resolution complexed with bovine pancreatic trypsin inhibitor.

The structure of tick anticoagulant peptide (TAP) has been determined by X-ray crystallography at 1.6 A resolution complexed with bovine pancreatic trypsin inhibitor (BPTI). The TAP-BPTI crystals are tetragonal, a = b = 46.87, c = 50.35 A, space group P41, four complexes per unit cell. The TAP molecules are highly dipolar and form an intermolecular helical array along the c-axis with a diameter of about 45 A. Individual TAP units interact in a head-to-tail fashion, the positive end of one molecule associating with the distal negative end of another, and vice versa. The BPTI molecules have a uniformly distributed positively charged surface that interacts extensively through 14 hydrogen bonds and two hydrogen bonded salt bridges with the helical groove around the helical TAP chains. Comparing the structure of TAP in TAP-BPTI with TAP bound to factor Xa(Xa) suggests a massive reorganization in the N-terminal tetrapeptide and the first disulfide loop of TAP (Cys5T-Cys15T) upon binding to Xa. The Tyr1(T)OH atom of TAP moves 14.2 A to interact with Asp189 of the S1 specificity site, Arg3(T)CZ moves 5.0 A with the guanidinium group forming a cation-pi-electron complex in the S4 subsite of Xa, while Lys7(T)NZ differs in position by 10.6 A in TAP-BPTI and TAP-Xa, all of which indicates a different pre-Xa-bound conformation for the N-terminal of TAP in its native state. In contrast to TAP, the BPTI structure of TAP-BPTI is practically the same as all those of previously determined structures of BPTI, only arginine and lysine side-chain conformations showing significant differences.

Kringle-kringle interactions in multimer kringle structures.

The crystal structure of a monoclinic form of human plasminogen kringle 4 (PGK4) has been solved by molecular replacement using the orthorthombic structure as a model and it has been refined by restrained least-squares methods to an R factor of 16.4% at 2.25 A resolution. The X-PLOR structure of kringle 2 of tissue plasminogen activator (t-PAK2) has been refined further using PROFFT (R = 14.5% at 2.38 A resolution). The PGK4 structure has 2 and t-PAK2 has 3 independent molecules in the asymmetric unit. There are 5 different noncrystallographic symmetry "dimers" in PGK4. Three make extensive kringle-kringle interactions related by noncrystallographic 2(1) screw axes without blocking the lysine binding site. Such associations may occur in multikringle structures such as prothrombin, hepatocyte growth factor, plasminogen (PG), and apolipoprotein [a]. The t-PAK2 structure also has noncrystallographic screw symmetry (3(1)) and mimics fibrin binding mode by having lysine of one molecule interacting electrostatically with the lysine binding site of another kringle. This ligand-like binding interaction may be important in kringle-kringle interactions involving non-lysine binding kringles with lysine or pseudo-lysine binding sites. Electrostatic intermolecular interactions involving the lysine binding site are also found in the crystal structures of PGK1 and orthorhombic PGK4. Anions associate with the cationic centers of these and t-PAK2 that appear to be more than occasional components of lysine binding site regions.

The isomorphous structures of prethrombin2, hirugen-, and PPACK-thrombin: changes accompanying activation and exosite binding to thrombin.

The X-ray crystal structure of prethrombin2 (pre2), the immediate inactive precursor of alpha-thrombin, has been determined at 2.0 A resolution complexed with hirugen. The structure has been refined to a final R-value of 0.169 using 14,211 observed reflections in the resolution range 8.0-2.0 A. A total of 202 water molecules have also been located in the structure. Comparison with the hirugen-thrombin complex showed that, apart from the flexible beginning and terminal regions of the molecule, there are 4 polypeptide segments in pre2 differing in conformation from the active enzyme (Pro 186-Asp 194, Gly 216-Gly 223, Gly 142-Pro 152, and the Arg 15-Ile 16 cleavage region). The formation of the Ile 16-Asp 194 ion pair and the specificity pocket are characteristic of serine protease activation with the conformation of the catalytic triad being conserved. With the determination of isomorphous structures of hirugen-thrombin and D-Phe-Pro-Arg chloromethyl ketone (PPACK)-thrombin, the changes that occur in the active site that affect the kinetics of chromogenic substrate hydrolysis on binding to the fibrinogen recognition exosite have been determined. The backbone of the Ala 190-Gly 197 segment in the active site has an average RMS difference of 0.55 A between the 2 structures (about 3.7 sigma compared to the bulk structure). This segment has 2 type II beta-bends, the first bend showing the largest shift due to hirugen binding. Another important feature was the 2 different conformations of the side chain of Glu 192. The side chain extends to solvent in hirugen-thrombin, which is compatible with the binding of substrates having an acidic residue in the P3 position (protein-C, thrombin platelet receptor). In PPACK-thrombin, the side chain of Asp 189 and the segment Arg 221A-Gly 223 move to provide space for the inhibitor, whereas in hirugen-thrombin, the Ala 190-Gly 197 movement expands the active site region. Although 8 water molecules are expelled from the active site with PPACK binding, the inhibitor complex is resolvated with 5 other water molecules.

Conformational rearrangements required of the V3 loop of HIV-1 gp120 for proteolytic cleavage and infection.

HIV gp120 is specifically cleaved at a single site in the V3 loop between Arg315 and Ala316 by thrombin. Previous observations by others have indicated that binding to CD4 enhances the rate of V3 loop cleavage, and that this cleavage is a prerequisite for HIV infection. Other observations also suggest that the cleavage site is in a type II beta-turn centered at Pro313-Gly314. However, our docking experiments indicate that this conformation cannot dock to thrombin and other trypsin-like serine proteases. Thus, based on the thrombin-bound conformation of peptide substrates, we propose that CD4 binding, at a site remote from the V3 loop, induces and stabilizes a trans to cis isomerization of the highly conserved residue Pro313, and that this conformational shift is a prerequisite for cleavage by a 'thrombin-like' cellular protease and subsequent infection.

Irreversible hypercapnia secondary to embolic occlusion of the pulmonary artery.

We describe a patient in whom extensive thromboembolic occlusion of the pulmonary arteries led to hypercapnia, in spite of a large increase in minute ventilation.

Structure of the non-covalent complex of prothrombin kringle 2 with PPACK-thrombin.

Prothrombin fragment 2 (the second kringle) has been co-crystallized with PPACK (D-Phe-Pro-Arg)-thrombin and the structure of the non-covalent complex has been determined and refined (R = 0.16) at 3.2 A resolution using X-ray crystallographic methods. The kringles interact with thrombin at a site that has previously been proposed to be the heparin binding region. The latter is a highly electropositive surface near the C-terminal helix of thrombin abundant in arginine and lysine residues. These form salt bridges with acidic side chains of kringle 2. Somewhat unexpectedly, the negative groups of the kringle correspond to an enlarged anionic center of the lysine binding site of lysine binding kringles such as plasminogen K1 and K4 and TPA K2. The anionic motif is DGDEE in prothrombin kringle 2. The corresponding cationic center of the lysine binding site region has an unfavorable Arg71Phe substitution but Lys35 is conserved. However, the folding of fragment 2 is different from that of prothrombin kringle 1 and other kringles: the second outer loop possesses a distorted two-turn helix and the hairpin beta-turn of the second inner loop pivots at V64 and D70 by 60 degrees. The Lys35 is located on a turn of the helix, which causes it to project into solvent space in the fragment 2-thrombin complex, thereby devastating the cationic center of the lysine binding site.(ABSTRACT TRUNCATED AT 250 WORDS)

The structure of recombinant plasminogen kringle 1 and the fibrin binding site.

The structure of recombinant (Hoover et al. Biochemistry, 1993; 32:10936-10944) plasminogen (PG) kringle 1 (K1) has been determined and refined at 2.48 A resolution to a crystallographic R value of 0.159. In addition, 71 water molecules and two chloride ions have been located. The folding of PGK1 is very similar to that of PGK4. The lysine/fibrin binding site, however, differs from that of both PGK4 and tissue-type PG activator (t-PA) K2 at the cationic centre. Although PGK1 can potentially have a doubly charged cationic centre utilizing Arg34 and Arg71, the side chain of Arg34 is outside of Arg71 in a solvent region and its guanidino group is flexibly disordered. Moreover, site specific mutagenesis studies show unequivocally that Arg34 can be changed to glutamine without affecting the binding ability of PGK1. Thus, PGK1 only has Arg71 at the cationic site, PGK4 has Lys35/Arg71 and t-PAK2 has only Lys33. The cationic site differences may result in subtle responses in the binding affinities of the kringles. The two chloride ions are located in the lysine binding site and effectively compensate the positive charges of the region. They also appear to be involved intermolecularly in a complex way in the crystal structure. Such intermolecular anionic interactions are also found in PGK4 and t-PAK2.

Computer vision analysis of somatic embryos of sweet potato [Ipomoea batatas (L.) Lam.] for assessing their ability to convert to plants.

Apical and axial shoot tips of sweet potato were cultured to produce somatic embryos that mature and develop into plants in basal nutrient medium. However, the lack of high regeneration efficiency is an impediment to the use of somatic embryos to produce synthetic seeds. Conversion experiments with mature embryos over a 20-day period revealed that 80-90% of the embryos formed roots but only 40-50% formed shoots. Using computer vision and canonical or Fisher discriminant function (CDA) analysis along with conversion results, it was possible to correctly classify competent embryos 40-50% of the time based on size features, 50-60% of the time based on shape features, and 55-60% of the time based on color features. Non-competent embryos were correctly classified 65-75%, 55-60%, and 70-75% of the time based on size, shape, and color, respectively. These results can be used effectively to identify and select competent embryos for improved regeneration efficiency.

A comparison of shoot-forming and non-shoot-forming somatic embryos of sweet potato [Ipomoea batatas (L.) Lam.] using computer vision and histological analyses.

Diagnostic structural features for competence to form shoots were tested among sweet potato embryos by combining morphological image capture (using a computer vision system) with anatomical analyses (using light microscopy). Five major morphological variants (`perfect', `near perfect', `limited/no meristematic activity', `disrupted internal anatomy', and `proliferating') were identified among torpedo- and cotyledonary-stage embryos. Among these, only the first two were found to be competent for conversion into plantlets. Lack of organized shoot development in somatic embryos of sweet potato was associated with the following abnormalities: lack of an organized apical meristem, sparcity of dividing cells in the apical region, flattened apical meristem, and multiple meristemoids and/or diffuse meristematic activity throughout the embryo. Diagnostic separation of most shoot-forming and non-shoot-forming torpedo and cotyledonary embryo variants was achieved.

Advanced upper airway obstruction caused by cervical goiter.

Goiters are an unusual cause of advanced upper airway obstruction. Previously described patients have been clearly symptomatic, and most have had substernal goiters. We present a patient with minimal symptoms with severe upper airway obstruction from a cervical goiter despite long-term therapy with thyroid hormone. Her spirometry exceeded criteria for urgent surgery. Patients with large goiters should have spirometry with flow-volume loop performed despite minimal or absent symptoms of respiratory distress.

Gabor spectra for Doppler echocardiography.

Doppler echocardiography on current ultrasonography machines makes use of short-time Fourier spectrograms (STFTs) to display the patterns of blood velocities in the heart chamber. From these sonologists infer the functional parameters, such as valve area, that have pathological significance. After mention of the lacuna in such an STFT display, the Gabor transform and associated Gabor spectrogram evaluation techniques are described. Finally, comparative views of ultrasound machine display with PC-based STFT and Gabor displays for two typical patients are shown, with inferences in support of the proposed Gabor display.

Teratocarcinosarcoma of the nose, paranasal sinuses and nasopharynx.

Teratomas affecting the head and neck are rare tumours of ambiguous origin. The benign form is seen in children and mostly affects the nasopharynx. Malignant tumours in the upper jaw have been reported rarely. They are almost exclusively seen in the adult male. They are highly aggressive tumours that are difficult to diagnose pre-operatively due to the varied histological patterns. Treatment options available are surgery, radiotherapy or a combination of both. Despite intensive treatment, the prognosis is still poor. A rare case of teratocarcinosarcoma of the nose, paranasal sinuses and nasopharynx in a 25-year-old male is presented. The tumour had a non-germ cell tumour origin. The clinical features, pathologic characteristics and treatment are detailed. It was managed by surgery, radiotherapy and chemotherapy.