A massive rock and ice avalanche caused the 2021 disaster at Chamoli, Indian Himalaya.

On 7 February 2021, a catastrophic mass flow descended the Ronti Gad, Rishiganga, and Dhauliganga valleys in Chamoli, Uttarakhand, India, causing widespread devastation and severely damaging two hydropower projects. More than 200 people were killed or are missing. Our analysis of satellite imagery, seismic records, numerical model results, and eyewitness videos reveals that ~27 × 106 cubic meters of rock and glacier ice collapsed from the steep north face of Ronti Peak. The rock and ice avalanche rapidly transformed into an extraordinarily large and mobile debris flow that transported boulders greater than 20 meters in diameter and scoured the valley walls up to 220 meters above the valley floor. The intersection of the hazard cascade with downvalley infrastructure resulted in a disaster, which highlights key questions about adequate monitoring and sustainable development in the Himalaya as well as other remote, high-mountain environments.

Correction: Castanea sativa (European Chestnut) Leaf Extracts Rich in Ursene and Oleanene Derivatives Block Staphylococcus aureus Virulence and Pathogenesis without Detectable Resistance.

[This corrects the article DOI: 10.1371/journal.pone.0136486.].

A framework for automated contour quality assurance in radiation therapy including adaptive techniques.

Contouring of targets and normal tissues is one of the largest sources of variability in radiation therapy treatment plans. Contours thus require a time intensive and error-prone quality assurance (QA) evaluation, limitations which also impair the facilitation of adaptive radiotherapy (ART). Here, an automated system for contour QA is developed using historical data (the 'knowledge base'). A pilot study was performed with a knowledge base derived from 9 contours each from 29 head-and-neck treatment plans. Size, shape, relative position, and other clinically-relevant metrics and heuristically derived rules are determined. Metrics are extracted from input patient data and compared against rules determined from the knowledge base; a computer-learning component allows metrics to evolve with more input data, including patient specific data for ART. Nine additional plans containing 42 unique contouring errors were analyzed. 40/42 errors were detected as were 9 false positives. The results of this study imply knowledge-based contour QA could potentially enhance the safety and effectiveness of RT treatment plans as well as increase the efficiency of the treatment planning process, reducing labor and the cost of therapy for patients.

SU-E-T-305: Limitations of Using DICOM Data for BrachyVision Treatment Plan Evaluation.

PURPOSE: To evaluate the accuracy of a real-time automated method of performing dosimetric quality assurance using Eclipse DICOM files for patients receiving HDR-brachytherapy and IMRT. METHODS: GYN patients are treated with concurrent high-dose rate brachtherapy and IMRT. The dosimetric parameters were obtained through an in-house QA program developed using Matlab. The DICOM files containing DVH data for organsat-risk (OAR) were analyzed Dosimetric data for 7 patients (total 42 fractions) were collected for bladder, rectum and sigmoid. The accuracy of the dosimetric parameters was estimated by comparing the parameters obtained from the DICOM based QA program and those in BrachyVision. RESULTS: The maximal dose values (Dmax) for the OARs obtained using the DICOM-based program are significantly smaller than those valued reported in BrachyVision by 36.2%-48.3%. The mean dose has a deviation from 1% - 2.4%. The dose for the volume of 2cc (D2cc) has a difference up to 7.6% for structures with the volume larger than 200 cc. The average difference of D2cc is 0.5% for structures less than 200 cc. We found that Eclipse BrachyVision only exports DVH data down to a volume equivalent to 1% of the maximum volume for a given structure. Therefore, the reported maximal dose values obtained from DICOM RT dose file do not accurately reflect the maximum dose in a treatment plan. This will also slightly affect the mean dose calculation and D2cc when the structure volume is larger than 200cc. CONCLUSIONS: The automatic QA tool based on DICOM files provides a quick retrieval of dose to organs-at-risk and coverage of targets. However, maximal dose to structures is not accurate due to the truncationof the DVH information contained in DICOM files.

The effect of amount of crude oil on extent of its biodegradation in open water- and sandy beach-laboratory simulations.

We examined the biodegradation of varying amounts of artificially weathered Alaskan North Slope crude oil in laboratory microcosm test systems that use natural seawater and simulate spills in open water and on sandy beaches. The model bioremediation treatment consisted of periodic applications of marine bacteria, selected to degrade n-alkanes and a range of aromatic compounds, suspended in a salts solution that supplied inorganic nitrogen and phosphorous. Beach microcosms dosed with low and high oiling lost an average of 22.5% and 11.3% oil weight, respectively. Open-water microcosms dosed with high and low oiling lost 19.1% and 2.9% oil weight, respectively. Thus, the lower doses of oil were more efficiently degraded. The model bioremediation treatment also affected a greater number of selected analytical endpoints in the lower-oil-dose than higher-dose experiments and the former showed more substantial degradation of recalcitrant components. Above a certain threshold oil concentration, bioremediation did not effectively remove oil. Below this threshold the distinction between active bioremediation treatment and intrinsic biodegradation of the controls was less prominent; i.e., fewer of the oil components were statistically depleted by remediation treatment relative to controls. Furthermore, the oil-dose range over which bioremediation was realized in these systems occurred at very low oiling levels. Thus, under the environmental conditions simulated in these microcosms, the effectiveness of bioremediation peaked over a rather narrow low-dose oiling range.

Site-directed mutations of human hemoglobin at residue 35beta: a residue at the intersection of the alpha1beta1, alpha1beta2, and alpha1alpha2 interfaces.

Because Tyr35beta is located at the convergence of the alpha1beta1, alpha1beta2, and alpha1alpha2 interfaces in deoxyhemoglobin, it can be argued that mutations at this position may result in large changes in the functional properties of hemoglobin. However, only small mutation-induced changes in functional and structural properties are found for the recombinant hemoglobins betaY35F and betaY35A. Oxygen equilibrium-binding studies in solution, which measure the overall oxygen affinity (the p50) and the overall cooperativity (the Hill coefficient) of a hemoglobin solution, show that removing the phenolic hydroxyl group of Tyr35beta results in small decreases in oxygen affinity and cooperativity. In contrast, removing the entire phenolic ring results in a fourfold increase in oxygen affinity and no significant change in cooperativity. The kinetics of carbon monoxide (CO) combination in solution and the oxygen-binding properties of these variants in deoxy crystals, which measure the oxygen affinity and cooperativity of just the T quaternary structure, show that the ligand affinity of the T quaternary structure decreases in betaY35F and increases in betaY35A. The kinetics of CO rebinding following flash photolysis, which provides a measure of the dissociation of the liganded hemoglobin tetramer, indicates that the stability of the liganded hemoglobin tetramer is not altered in betaY35F or betaY35A. X-ray crystal structures of deoxy betaY35F and betaY35A are highly isomorphous with the structure of wild-type deoxyhemoglobin. The betaY35F mutation repositions the carboxyl group of Asp126alpha1 so that it may form a more favorable interaction with the guanidinium group of Arg141alpha2. The betaY35A mutation results in increased mobility of the Arg141alpha side chain, implying that the interactions between Asp126alpha1 and Arg141alpha2 are weakened. Therefore, the changes in the functional properties of these 35beta mutants appear to correlate with subtle structural differences at the C terminus of the alpha-subunit.

Analysis of the CC chemokine receptor 3 gene reveals a complex 5' exon organization, a functional role for untranslated exon 1, and a broadly active promoter with eosinophil-selective elements.

To understand the regulation of CC chemokine receptor 3 (CCR3) expression, its gene structure and promoter have been characterized. The CCR3 gene contains 4 exons that give rise to multiple messenger RNA (mRNA) species by alternative splicing. Exon 1 is present in all transcripts, whereas exon 2 or 3 is present at low frequency (< 10%). Exon 4 contains the open reading frame and 11 bp of the 5' untranslated region. Northern analysis revealed 4 species of CCR3 mRNA. Direct sequencing revealed that the first 1 kb of the promoter and exon 1 contained only one mutation in 19 individuals, indicating that the CCR3 promoter and exon 1 are conserved between individuals. The first 1.6 kb of the 5' flanking region of exon 1 contained promoter elements including a TATA box and motifs for myeloid transcription factors and had strong promoter activity in eosinophilic, lymphoid, myeloid, and respiratory epithelial cell lines. Deletion analysis revealed differential regulation of the CCR3 promoter in eosinophilic and epithelial cells suggesting the presence of lineage-specific elements. Interestingly, exon 1 enhanced the activity of the promoter and this effect was especially prominent in eosinophilic cells. Thus, the human CCR3 gene has a complex 5' exon structure, a conserved promoter with strong activity in multiple cell types, and a functional 5' untranslated exon.

Too much of a good thing: overuse injuries of the knee.

Overuse injuries constitute a distinct group of abnormalities arising from excessive stress, repeated microtrauma, inadequate injury repair, or pathologic motion of the knee. Chronic pain resulting from overuse injuries may progress to the point that the patient can no longer perform the inciting activity. MR image appearances of the more common overuse syndromes involving the soft tissues surrounding the knee are presented, pertinent anatomic features are reviewed, and the role of MR imaging in patient management in these disorders is discussed.

Structural and functional properties of human hemoglobins reassembled after synthesis in Escherichia coli.

Human hemoglobin produced in the Escherichia coli coexpression system of Hernan et al. [(1992) Biochemistry 31, 8619-8628] has been transformed into a functionally homogeneous protein whose properties closely approximate those of normal hemoglobin A. Both of the alpha and beta chains of this hemoglobin contain a valine-methionine substitution at position 1 in order to accommodate the difference in specificity of the protein-processing enzymes of procaryotes. Despite extensive purification, functional homogeneity of the E. coli expressed hemoglobin was achieved only by the complete disassembly of the hemoglobin into its component alpha and beta globins and their reassembly in the presence of hemin. The kinetics of CO combination and the thermodynamics of O2 binding and cooperativity of the reassembled alphaV1M-betaV1M hemoglobin closely approximate those of HbA. The alpha globin obtained from the E. coli expressed hemoglobin was also combined with normal human beta chains and hemin to form the alphaV1M variant. The alpha+M variant of HbA, in which the normal N-terminal valine of the alpha chains is preceded by a methionine residue, was prepared by the same procedure. The kinetics of the reactions of CO with the alphaV1M and alpha+M variants are similar to those for HbA. The equilibria of oxygen binding to alphaV1M and HbA are similar whereas alpha+M exhibits a significantly higher oxygen affinity. The three-dimensional structures of alphaV1M and alpha+M offer an explanation for the latter affinity difference. Although the structures of alphaV1M and HbA, which have been determined by X-ray crystallography, are virtually indistinguishable except at the N-terminal residues, that of alpha+M indicates the displacement of a solvent molecule, possibly a chloride ion, from arginine 141alpha. Such an alteration in an anion binding site could result in increased oxygen affinity.

High-resolution crystal structures of human hemoglobin with mutations at tryptophan 37beta: structural basis for a high-affinity T-state,.

The high-resolution X-ray structures of the deoxy forms of four recombinant hemoglobins in which Trp37(C3)beta is replaced with Tyr (betaW37Y), Ala (betaW37A), Glu (betaW37E), or Gly (betaW37G) have been refined and analyzed with superposition methods that partition mutation-induced perturbations into quaternary structure changes and tertiary structure changes. In addition, a new cross-validation statistic that is sensitive to local changes in structure (a "local Rfree" parameter) was used as an objective measure of the significance of the tertiary structure changes. No significant mutation-induced changes in tertiary structure are detected at the mutation site itself for any of the four mutants studied. Instead, disruption of the intersubunit contacts associated with Trp37(C3)beta results in (1) a change in quaternary structure at the alpha1beta2 interface, (2) alpha subunit tertiary structure changes that are centered at Asp94(G1)alpha-Pro95(G2)alpha, (3) beta subunit tertiary structure changes that are located between residues Asp99(G1)beta and Asn102(G4)beta, (4) increased mobility of the alpha subunit COOH-terminal dipeptide, and (5) shortening of the Fe-Nepsilon2His(F8) bond in the alpha and beta subunits of the betaW37G and betaW37E mutants. In each case, the magnitude of the change in a particular structural parameter increases in the order betaW37Y < betaW37A < betaW37E approximately betaW37G, which corresponds closely to the degree of functional disruption documented in the preceding papers.

Structure and oxygen affinity of crystalline des-his-146beta human hemoglobin in the T state.

To correlate directly structure with function, the oxygen affinity and the three-dimensional structure of crystals of the T quaternary state of des-His-146beta human hemoglobin have been determined by polarized absorption microspectrophotometry and x-ray diffraction crystallography. In des-His-146beta, the COOH-terminal histidine residues of the beta chains of hemoglobin A have been removed. Oxygen binding to crystalline des-His hemoglobin is non-cooperative and independent of pH. The oxygen affinity is 1.7-fold greater than that of the crystalline state of hemoglobin A. Removal of His-146beta results in a small movement of the truncated COOH-terminal peptide and in a very small change in quaternary structure. Previously, similar studies on T state crystals of des-Arg-141alpha hemoglobin showed that removal of the COOH termini of the alpha chains results in much larger effects on oxygen affinity and on quaternary structure. Kinetic studies in solution reveal that at pH 7.0, the rates of CO combination with deoxygenated des-His-146beta in the absence and presence of inositol hexaphosphate are 2.5- and 1.3-fold, respectively, more rapid than for hemoglobin A. The values for des-Arg are 7.6- and 3.9-fold. The properties of the T state of hemoglobin both in the crystal and in solution are influenced to a greater degree by the interactions associated with Arg-141alpha than those associated with His-146beta.

Structure and oxygen affinity of crystalline desArg141 alpha human hemoglobin A in the T state.

The correlation of a protein structure determined crystallographically to its functional properties determined in solution can be an extremely complex problem due to potential differences of protein conformational flexibility in the two physical states. A more direct approach to the correlation of structure with function is to examine both the structure and the function of a protein in the same crystalline environment. In this paper, the structural and functional properties of T state desArg hemoglobin (human hemoglobin modified by removal of the alpha-chain COOH-terminal residue, Arg141 alpha) have been studied in the same crystal form by high resolution X-ray diffraction methods and by polarized absorption microspectrophotometry. Specifically, the crystal structure of deoxygenated desArg human hemoglobin has been refined at a 2.1 A resolution using crystals grown at low salt concentration from solutions of polyethylene glycol. The loss of Arg141 alpha and all of the salt bridges in which it participates is associated with subtle structural perturbations of the alpha-chains which include an increase in the conformational flexibility of both the NH2 and COOH-terminal peptides. Although the heme pockets appear unchanged and even the side-chain of Tyr140 is oriented nearly as in HbA, the functional characterization by microspectrophotometric measurements indicates that crystals of desArg hemoglobin bind oxygen with an affinity which is roughly 15-fold greater than that of crystals of human hemoglobin A. There is no alkaline Bohr effect or effect of chloride ions, but an acid Bohr effect is observed. The oxygen affinities measured along two principal axes of the crystals differ by 25%, indicating heterogeneity in the affinities of the oxygen binding sites. This finding and the measured Hill coefficient of unity suggest significant cooperativity in the binding of oxygen in these crystals. The origins of the observed heterogeneity and the implied cooperativity are unknown.

Effect of accessory sex gland fluid from bulls of differing fertilities on the ability of cauda epididymal sperm to penetrate zona-free bovine oocytes.

The ability of accessory sex gland fluid to affect the fertility of cauda epididymal sperm was evaluated for 10 bulls that ranged in fertility from 6.2% below to 6.0% above the average fertility of bulls at artificial breeding cooperatives. Cauda epididymal sperm collected from indwelling vasa deferentia catheters and cauda epididymal sperm exposed to accessory sex gland fluid from the same bull were compared on the basis of their rates of in vitro penetration of zona-free oocytes after heterospermic insemination. Incubation of cauda epididymal sperm with accessory sex gland fluid significantly enhanced the ability to penetrate oocytes, and bull fertility affected the magnitude of this improvement. For bulls of average and higher fertility, the positive influence of accessory sex gland fluid on penetrating ability of sperm was highly significant (p < 0.0001). Accessory sex gland fluid from bulls of below-average fertility also improved the penetrating ability of cauda epididymal sperm, although not significantly (p = 0.07). Heterospermic competitions compared the penetrating ability of cauda epididymal sperm exposed to homologous accessory sex gland fluid with a portion of the same sperm population incubated in heterologous accessory sex gland fluid from a bull of contrasting fertility. In experiments involving sperm from 12 different bulls, paired in 42 fertile/subfertile combinations, samples of cauda epididymal sperm mixed with accessory sex gland fluid from the higher-fertility bulls had greater oocyte-penetrating ability than when aliquots of that sample were mixed with accessory gland fluid from lower-fertility bulls (p < 0.0001).(ABSTRACT TRUNCATED AT 250 WORDS)

Hemodynamics and wall shear rate in the abdominal aorta of dogs. Effects of vasoactive agents.

Vasoactive drugs are known to affect impedance (pressure/flow) and vessel wall motion in arteries. The nonlinear theory of oscillatory flow in straight elastic vessels indicates that wall shear rate is affected by changes in impedance phase angle and wall motion. To test whether wall shear rate depends on impedance phase angle and wall motion in vivo, wall shear rate was measured in the abdominal aorta of anesthetized dogs by using a flush-mounted hot-film anemometer, and the hemodynamic state was characterized by pressure, flow, and vessel dimension measurements. Vasodilators (nitroprusside and isoproterenol) and vasoconstrictors (angiotensin II and norepinephrine) were administered acutely, and the responses of wall shear rate and hemodynamics were determined. In the control state (no drugs), peak wall shear rate was 1835 +/- 153 s-1 (mean +/- SEM). The vasodilators induced large increases in impedance phase angle and wall motion concomitant with large increases in peak wall shear rate (62.4 +/- 20.4% for nitroprusside and 68.9 +/- 28.3% for isoproterenol), which were not predicted accurately by Womersley's theory of oscillatory flow in a rigid vessel or the nonlinear theory of oscillatory flow in an elastic vessel, with measured flow and vessel dimension used as inputs. The vasoconstrictors induced small decreases in impedance phase angle and wall motion and small changes in peak wall shear rate (increase, 30.5 +/- 8.0% for norepinephrine; decrease, 18.2 +/- 7.1% for angiotensin II), which were predicted accurately by Womersley's theory. The present study shows that vasoactive drugs, particularly vasodilators, can have significant effects on wall shear rate (stress) in the abdominal aorta that appear to be related to changes in impedance phase angle and vessel wall motion. However, the effects on wall shear rate are not predicted accurately by straight-tube theory.

Accommodation of insertions in helices: the mutation in hemoglobin Catonsville (Pro 37 alpha-Glu-Thr 38 alpha) generates a 3(10)-->alpha bulge.

Hemoglobin Catonsville is a mutation of human hemoglobin (an alpha 2 beta 2 tetramer) in which a glutamate residue is inserted into the first turn of a highly conserved 3(10) helix (the C helix) of each alpha subunit. In theory, amino acid insertions (or deletions) in protein helices can be accommodated via two distinct mechanisms. One, termed the register shift mechanism, preserves the geometry of the helix while requiring all of the residues on one flank of the insertion site to rotate by 100 degrees in the case of an alpha helix or by 120 degrees in the case of a 3(10) helix. The other, termed the bulge (or indentation) mechanism, distorts the local geometry of the helix but does not alter the helix register. High-resolution X-ray diffraction analysis of deoxyhemoglobin Catonsville shows that the inserted residue is accommodated as a bulge, demonstrating that this is a viable mechanism. (In contrast, no such evidence is yet available for the register shift mechanism.) More specifically, the insertion converts one turn of the C helix from 3(10) geometry to alpha helix-like geometry, raising the possibility that a common mechanism for accommodating insertions and deletions within helices may involve localized interconversions between 3(10), alpha, and pi helical structures.

High-resolution X-ray study of deoxy recombinant human hemoglobins synthesized from beta-globins having mutated amino termini.

The crystal structures of three mutant hemoglobins reconstituted from recombinant beta chains and authentic human alpha chains have been determined in the deoxy state at 1.8-A resolution. The primary structures of the mutant hemoglobins differ at the beta-chain amino terminus. One mutant, beta Met, is characterized by the addition of a methionine at the amino terminus. The other two hemoglobins are characterized by substitution of Val 1 beta with either a methionine, beta V1M, or an alanine, beta V1A. All the mutation-induced structural perturbations are small intrasubunit changes that are localized to the immediate vicinity of the beta-chain amino terminus. In the beta Met and beta V1A mutants, the mobility of the beta-chain amino terminus increases and the electron density of an associated inorganic anion is decreased. In contrast, the beta-chain amino terminus of the beta V1M mutant becomes less mobile, and the inorganic anion binds with increased affinity. These structural differences can be correlated with functional data for the mutant hemoglobins [Doyle, M. L., Lew, G., DeYoung, A., Kwiatkowski, L., Noble, R. W., & Ackers, G. K. (1992) Biochemistry preceding paper is this issue] as well as with the properties of ruminant hemoglobins and a mechanism [Perutz, M., & Imai, K. (1980) J. Mol. Biol. 136, 183-191] that relates the intrasubunit interactions of the beta-chain amino terminus to changes in oxygen affinity. Since the structures of the mutant deoxyhemoglobins show only subtle differences from the structure of deoxyhemoglobin A, it is concluded that any of the three hemoglobins could probably function as a surrogate for hemoglobin A.(ABSTRACT TRUNCATED AT 250 WORDS)

Hemoglobin Thionville. An alpha-chain variant with a substitution of a glutamate for valine at NA-1 and having an acetylated methionine NH2 terminus.

In hemoglobin (Hb) Thionville, the substitution of a glutamic acid for the alpha-chain NH2-terminal valine inhibits the cleavage of the initiator methionine which is then acetylated. The elongation of the alpha-chain NH2 terminus modifies the three-dimensional structure of hemoglobin at a region that is known to have an important role in the allosteric regulation of oxygen binding. Relative to Hb A, Hb Thionville has a lower affinity for oxygen, and the heterotropic allosteric effects of protons, chloride, and bezafibrate are reduced. In contrast, the response to 2,3-diphosphoglycerate is normal. Analysis of oxygen equilibrium data within the framework of the two-state allosteric model indicates that the structure of deoxy Hb Thionville is stabilized relative to that of deoxy Hb A. The x-ray crystal structure of deoxy Hb Thionville shows that the glutamate side chain extends away from the alpha 1-alpha 2 interface, whereas the methionine side chain (which has two conformations) extends into the alpha 1-alpha 2 interface, physically displacing chloride and bezafibrate. The increased stability of deoxy Hb Thionville is due to new intrasubunit and intersubunit contacts made by the methionine. These interactions replace the indirect contacts, made through bound chloride ions, that Val-1 alpha normally contributes to the alpha 1-alpha 2 interface.