bluuebunny/crossref_metadata_2025 huggingface dataset:
Antecedents and Consequences of Corporatization: An Empirical Analysis of German Public Hospitals
Authors: Lindlbauer Ivonne , Winter Vera , Schreyögg Jonas
Published: June 2015

The idea of privatizing or corporatizing public enterprises to improve organizational performance is a central tenet of the new public management movement. Yet while privatization represents a well-established subject of inquiry, corporatization remains a research field scarcely trodden, leaving the public debate bereft of sound empirical evidence. Building on the contingency theory, principal-agent theory, and corporatization literatures, the purpose of this study is to help bridge this research gap by empirically assessing the postulated relationships on the antecedents and consequences of corporatization. Choosing public hospitals as research subjects, it builds on a comprehensive longitudinal dataset and proceeds in four steps: calculating efficiency scores using data envelopment analysis; investigating the antecedents of corporatization with logistic regression; constructing an appropriate control group consisting of noncorporatized public-law hospitals using genetic matching; and comparing changes in efficiency between corporatized and noncorporatized hospitals by means of a difference-in-difference approach. The results indicate that public-law hospitals were significantly more likely to be corporatized under certain circumstances, namely, in areas with a higher degree of spatial competition, during the years around a major change in the reimbursement system (2003–2005), and if they were legally dependent entities. In contrast, having lower baseline efficiency had no significant effect on the likelihood of corporatization. Furthermore, corporatization had a significantly positively effect on the efficiency of previously public-law hospitals. This effect was higher for hospitals that had been legally independent than for those that had been legally dependent. In sum, corporatization is likely an effective alternative to privatization, a finding that leads to a range of implications for practice and research.
Spinal and Epidural Anesthesia in Patients With Recent Stable Fractures of Vertebral Column
Authors: Gurajala Indira , Iyengar Raju , Durga Padmaja , Gopinath Ramachandran
Published: June 2015

Background:

The use of central neuraxial block (CNB) in patients with spinal injuries with or without spinal cord injury continues to be a contentious issue due to paucity of evidence supporting or refuting its use. There are only a few case reports reporting the use of the technique in these patients. We performed a retrospective record review of patients who underwent neuraxial blockade for lower limb orthopedic surgery in the presence of coexisting recent spine injury (defined as spine injury within 1 month) to assess the occurrence of postoperative deterioration of spinal cord function or occurrence of new spinal cord dysfunction.

Materials and Methods:

The hospital records of patients with recent stable traumatic fractures of the vertebral column who underwent lower limb orthopedic surgery under CNB from January 2010 to December 2013 were reviewed. Data collected included age, sex, level of fracture, number of vertebrae injured, presence of neurological deficits, interval between injury and surgery, number of surgeries, level of CNB, number of vertebral segments between the site of injury and CNB, position of patient used for CNB and surgery, and perioperative adverse hemodynamic events. All patients underwent detailed postoperative neurological examination and any deterioration or occurrence of new spinal cord dysfunction was noted.

Results:

Nineteen patients underwent 21 CNBs for lower limb orthopedic procedures. There were 12 men and 7 women. Thoracolumbar area (18/19) was the commonest site of fractures. Two patients had neurological deficits due to cervical spine trauma. More than 50% of the patients had multiple bone fractures and nearly 30% had associated nonorthopedic trauma. Six patients underwent surgery within the first week (4 to 7 d) after trauma. In 80% of the patients, there was a gap of atleast 2 vertebrae between the level of injury and CNB administration. There were no perioperative adverse hemodynamic events requiring prolonged inotropic support. None of the patients had neurological deterioration or new changes.

Conclusions:

Spinal and epidural anesthesia in patients with recent stable fractures of the spine was not associated with adverse neurological events. The findings of this study may be particularly relevant to patients with recent stable vertebral fractures who require surgery but present with conditions that place them at high risk for general anesthesia.
Presentation of Adolescent Idiopathic Scoliosis: The Bigger the Kid, the Bigger the Curve
Authors: Goodbody Christine M. , Sankar Wudbhav N. , Flynn John M.
Published: June 2015

Background:

It is our clinical suspicion that children with higher body mass index (BMIs) who are diagnosed with scoliosis tend to have larger curves on presentation. The purpose of this study was to determine the effect of BMI on severity of curve at initial presentation of adolescent idiopathic scoliosis.

Methods:

This is a retrospective, descriptive cohort study of consecutive patients age 10 or greater referred to a single large tertiary care center with concern for spinal asymmetry. Patients were separated into 3 BMI categories as measured on the presenting visit: normal weight—≥5th and <85th percentile, overweight—≥85th and <95th percentile, and obese—≥95th percentile. In addition to demographic information, data collected included BMI, curve magnitude, curve location, Risser stage, and where or by whom spinal asymmetry was noted.

Results:

A total of 150 patients, 50 in each the normal weight, overweight, and obese categories, were included in this study. Average curve at presentation for normal weight patients was 18.1 degrees, for overweight patients 23.9 degrees (P=0.02), and for obese patients 24.5 degrees (P=0.02). As compared with the normal weight group, odds ratio of presenting with a curve of 40 degrees or above was 10.8 for the overweight group (95% confidence interval, 1.3-88.5, P=0.03) and 12.2 for the obese group (95% confidence interval, 1.5-99.8, P=0.02). Assuming a cut-off of 45 degrees as surgical range, no normal weight patients presented in surgical range (0%), but 7/50 (14%, P=0.01) overweight and 8/50 (16%, P<0.01) obese patients did. Moreover, higher BMI patients were significantly more likely to present at a higher degree of skeletally maturity, with an average Risser of 1.8 for normal weight patients, 2.7 (P=0.01) for overweight patients, and 2.9 (P=0.01) for obese patients.

Conclusions:

Overweight and obese patients with adolescent idiopathic scoliosis present at significantly larger curve magnitudes and significantly higher degrees of skeletal maturity. Moreover, these patients were significantly more likely to present with very large curves and, in our study, all patients presenting with a surgical range curve were either overweight or obese.

Level of Evidence:

Level III—Retrospective case-control.
Total Auricular Rehabilitation
Authors: Littlefield Philip D. , Tolisano Anthony M. , Sabol Jennifer V. , Herberg Matthew E. , Coppit George L.
Published: June 2015

Objective:

The aim of the study was to describe 3 cases of total auricular rehabilitation, including the novel use of iliac crest bone grafts to support bone-anchored auricular prostheses.

Study Design:

This study is a retrospective case series from a single institution.

Results:

Three cases with large lateral temporal bone and soft tissue defects were successfully treated with total auricular rehabilitation. Rehabilitation included the following: soft tissue coverage with an anterolateral thigh microvascular free flap, iliac crest–free bone graft with staged placement of a bone-anchored auricular prosthesis into the bone graft, and audiologic rehabilitation with a bone-anchored hearing aid (BAHA).

All of the cases with grafts and flaps survived and were without significant donor site morbidity. Bone-anchored hearing aid abutment skin overgrowth was seen in 2 cases and was revised under local anesthesia. All of the patients had expected functional recovery on postoperative audiologic testing. Each patient continues to consistently wear his/her auricular prosthesis and BAHA during 3 years of follow-up.

Conclusions:

Total auricular rehabilitation is a complex task involving reconstruction of extensive soft tissue defects, bony defects, and the hearing apparatus. Acceptable cosmetic and functional outcomes and high patient satisfaction is possible in committed patients.
Evaluation of the Cortical Bone Reaction Around of Implants Using a Single-Use Final Drill
Authors: Gehrke Sergio Alexandre
Published: June 2015

Objectives:

This study was designed to compare the cortical bone reaction following traditional osteotomy or the use of a single-use final drill in the osseointegration of implants in the tibia of rabbits.

Materials and Methods:

For this study, 48 conical implants, of standard surface type and design and manufactured by the same company, were inserted into the tibiae of 12 rabbits and removed after 30 or 60 days for histologic analysis. Two test groups were prepared according to the drill sequence used for the osteotomy at the preparation sites: in the control group was used a conventional drill sequence with several uses, whereas the test group (tesG) used a single-use final drill. The bone-to-implant contact and qualitative factors of the resulting cortical bone were assessed.

Results:

Both techniques produced good implant integration. Differences in the linear bone-to-implant contact were observed between the drilling procedures as time elapsed in vivo, with the tesG appearing to have clinical advantages. Both groups exhibited new bone in quantity and in quality; however, the tesG exhibited a higher level of new bone deposition than the control group.

Conclusions:

Within the limitations of this study, the findings suggest that the use of a single-use final drill leads to better and faster organization of the cortical bone area during the evaluated period and may avoid the possible problems that can be caused by worn drills.
High-Energy Traumatic Maxillofacial Injury
Authors: Christensen Jacob , Sawatari Yoh , Peleg Michael
Published: June 2015

High-energy blunt or penetrating impact leads to great variability in facial injury patterns. Although the mechanism, pattern, and distribution of forces vary, the resultant damage to hard and soft tissues requires dedicated planning and execution of debridement and reconstructive procedures. This article evaluates the initial management of patients sustaining high-energy facial impact injuries resulting in one or more comminuted or displaced facial fractures, with accompanying severe facial lacerations and/or soft tissue defects and avulsion injuries. Seventy-three patients met the criteria for high-energy traumatic injuries at Jackson Memorial/University of Miami Medical Center between 2003 and 2013 and are included in this article. Thirty-nine patients sustained one or more gunshot wounds to the face, and 34 patients were involved in high-speed motor vehicle collisions; all patients met our criteria for high-energy trauma. The treatment protocol for these injuries involves meticulous surgical exploration and assessment, aggressive debridement, early definitive reduction/fixation, and reconstruction as necessary.
A Hypothesis for the Pathologic Mechanism of Idiopathic Exophthalmos Based on Computed Tomographic Evaluations
Authors: Takada Keiko , Sakamoto Yoshiaki , Shimizu Yusuke , Nagasao Tomohisa , Kishi Kazuo
Published: June 2015

The causes of idiopathic exophthalmos were still unknown. We used computed tomography to compare the orbital structures of patients with idiopathic exophthalmos and those of a healthy Japanese population. A total of 18 orbits (ranged 17–52 years) in idiopathic exophthalmos and 334 normal orbits (ranged 17–59 years) were included. On computed tomography, the eyeball and orbit sizes, lateral wall thickness and length, perpendicular distance from the interzygomatic line to the medial orbital rim, and the nasal cavity width were measured. No significant differences in eyeball or orbit sizes were found between the idiopathic exophthalmos and control groups (P > 0.05). In contrast, the mean lateral wall thickness of the idiopathic exophthalmos group was significantly thicker than that of the control group (P < 0.01). The lateral wall length was shorter with significant difference (P < 0.05). The perpendicular distance and the width of the nasal cavity in the idiopathic exophthalmos group were longer with significant difference (P < 0.05). The cause of idiopathic exophthalmos is compression of orbital contents by the medial wall expansion. The force of expansion of medial wall also influences the zygoma according to Wolff law.
Sir William Arbuthnot Lane and His Contributions to Plastic Surgery
Authors: Breakey Richard William F. , Mulliken John B.
Published: June 2015

Surgical subspecialties were just emerging at the turn of the 20th Century, before this time, general surgeons had to adjust their operative skills to address disorders throughout the body. Sir William Arbuthnot Lane was a British surgeon, whose restless mind led him to wander throughout the field of general surgery and beyond. Although controversial, he advanced in the repair of cleft lip and palate, introduced the “no touch” operative technique, internal fixation of fractures, and is credited as the first surgeon to perform open massage of the heart. During The Great War, he established the British Plastic Surgery unit at Sidcup and delegated the care of facial and jaw injuries to young Major Harold Gillies. Lane later founded The New Health Society, an organization that stimulated the natural food movement. Sadly, in his latter years Lane's thinking drifted further away from with the times and his professional credibility waned. Nevertheless, Lane's variegated life is of sufficient interest to deserve reassessment.
Severe Pediatric Midface Trauma
Authors: Davidson Edward H. , Schuster Lindsay , Rottgers S. Alex , Smith Darren M. , Naran Sanjay , Goldstein Jesse A. , Losee Joseph E.
Published: June 2015

Severe pediatric facial trauma is characterized by multiple, comminuted, and unstable fractures, frequently necessitating operative intervention. Disruption of facial growth is a primary concern in the long-term sequelae of such conditions. Children suffering from midface fractures were followed over time in a long-term growth and development study. Lateral cephalograms at longest-term follow-up were traced, digitized, and averaged. Seven landmarks of the midface (A point, ANS, orbitale, bridge of nose, distal U6, upper lip, stomion superius) were identified for comparative measurements with age and sex-matched superimposed Bolton norms as controls. Differences in x and y axes between test and control metrics were measured. Clinical significance was defined as a 2-mm discrepancy from the norm. Statistical significance for each patient was determined using t tests of the x and y arrays of patient values versus normal controls. Seven patients met the inclusion criteria with mean age of 8.9 years at the time of injury. Mean cephalometric follow-up was 4.6 years (range 2–10 years). Six out of 7 patients (86%) showed clinically significant impairment in growth in horizontal (29%), vertical (29%), or both planes (29%). T Tests confirmed statistical significance (P ≤ 0.05) for all clinically significant differences. Mean deficiency in growth for all landmarks was 3.7 mm (range −4.0 to 13.7 mm) in the x axis and 2.9 mm (range −1.1 to 8.8 mm) in the y axis. Severe pediatric midface trauma often results in compromised bone growth and permanent facial deformity. New methodologies of management that better allow for growth are needed.
The Effect of Subcutaneous Platelet-Rich Plasma Injection on Viability of Auricular Cartilage Grafts
Authors: Bulam Hakan , Ayhan Suhan , Yilmaz Guldal , Sezgin Billur , Sibar Serhat , Tuncer Serhan , Findikcioglu Kemal , Latifoglu Osman
Published: June 2015

Introduction:

Although cartilage grafts are frequently used for structural integrity and volume restoration, one of the main concerns dealing with cartilage grafting is gradual volume loss and unpredictable viability rates of cartilage grafts. Platelet-rich plasma (PRP) is a well known platelet concentrate reported to enhance cartilage repair and stimulates chondrocyte proliferation and matrix biosynthesis. The purpose of the current study was to investigate the effect of subcutaneous PRP injection on improving the viability of cartilage grafts.

Materials and Methods:

Six circular cartilage grafts were obtained from auricular cartilages of 6 New Zealand white rabbits. Cartilage grafts were prepared in 3 forms: block, crushed, and crushed/wrapped with Surgicel (Surgical, Ethicon, Somerville, NJ). Grafts were placed to 6 dorsal subcutaneous pockets and pockets were closed. Autologous PRP was prepared and injected subcutaneously into the pockets of experiment groups. At the end of 8 weeks, cartilage grafts were removed. Cartilage mass reduction rates were measured. Resorption rates of cartilage grafts and formation of fibroelastic and bone tissue were microscopically evaluated.

Results:

All of the cartilage grafts lost significant weight. Viability scores of block cartilages were higher than crushed cartilages. Although less weight loss rates and higher histopathologic scores were obtained in subcutaneously PRP injected cartilage graft groups, these results were not statistically significant.

Conclusions:

Although our study gives a new insight about increasing the viability of cartilage grafts, the subcutaneous PRP injection did not result in improving the viability of cartilage grafts in this experimental design.
Image-Guided Sinus Surgery in Sinonasal Pathologies With Skull Base/Orbital Erosion
Authors: Al-Qudah Mohannad
Published: June 2015

Objective:

The aim of the study was to review the use and outcomes of image-guided sinus surgery (IGSS) in sinonasal pathologies with skull base/orbital erosion without intracranial or intraorbital extension.

Method:

A retrospective charts and medical records review was performed for 474 consecutive sinonasal surgeries performed by a single surgeon at tertiary, academic center from August 2010 to December 2013.

Result:

Fourteen subjects (mean age 27 years; 8 men and 6 women) were identified. Mucocele and tumor were the most common pathological indication for IGSS use in this case series. Orbital wall erosion was detected in 57%, skull base in 29%, and both sites in 14%. The average blood loss was 80 mL, the average operative time was 190 minutes, and the average hospital stay was 3 days. There was no major intra- or postoperative complications. Two patients required revision endoscopic sinus surgery. The mean follow-up was 14 months (range 8–36 months).

Conclusion:

Image-guided sinus surgery alone is safe and effective procedure for a variety of sinonasal pathologies with orbital and skull base erosion.
Occurrence of Pneumatic Cavities Surrounding the Temporomandibular Joint
Authors: Sen Yilmaz Berza , Aksakalli Sertac , Birlik Muhammet , Dadasli Ferit , Bolukbasi Esra , Aytugar Emre
Published: June 2015

Objectives:

The aim of this study was to investigate the occurrence, the location, and the characteristics of the pneumatic cavities (PCAs) surrounding the temporomandibular joint (TMJ) by using cone-beam computed tomography.

Methods:

A retrospective study was performed by using the three-dimensional data archives from Faculty of Dentistry, Bezmialem University, Istanbul, Turkey. The age and sex had been previously recorded for all of the patients. The location and the morphologic characteristics of the PCAs were documented.

Results:

Pneumatic cavities were found in 18 patients (15%): 11 women (61%) and 7 men (39%). Eleven (57.9%) of the patients showed unilocular pneumatic air cells and 8 (42.1%) of them showed multilocular ones. The unilateral-to-bilateral ratio was 2.3:1. The age range was 8 to 76 years (mean 29.5 ± 21.86 years), and the female-to-male ratio was 1.57:1.

Conclusion:

Cone-beam computed tomography provides images without superimposition that allows accurate and easy evaluation of the PCAs surrounding the TMJ. Our results suggest that the occurrence of PCAs is higher than has been previously reported; therefore, it is recommended for clinicians who are planning to perform TMJ surgery to think about the PCAs to understand the exact morphology for avoiding intraoperative complications.
A Three-Dimensional Statistical Average Skull
Authors: Teshima Tara Lynn , Patel Vaibhav , Mainprize James G. , Edwards Glenn , Antonyshyn Oleh M.
Published: June 2015

Purpose:

The utilization of three-dimensional modeling technology in craniomaxillofacial surgery has grown exponentially during the last decade. Future development, however, is hindered by the lack of a normative three-dimensional anatomic dataset and a statistical mean three-dimensional virtual model. The purpose of this study is to develop and validate a protocol to generate a statistical three-dimensional virtual model based on a normative dataset of adult skulls.

Method:

Two hundred adult skull CT images were reviewed. The average three-dimensional skull was computed by processing each CT image in the series using thin-plate spline geometric morphometric protocol. Our statistical average three-dimensional skull was validated by reconstructing patient-specific topography in cranial defects. The experiment was repeated 4 times. In each case, computer-generated cranioplasties were compared directly to the original intact skull. The errors describing the difference between the prediction and the original were calculated.

Results:

A normative database of 33 adult human skulls was collected. Using 21 anthropometric landmark points, a protocol for three-dimensional skull landmarking and data reduction was developed and a statistical average three-dimensional skull was generated. Our results show the root mean square error (RMSE) for restoration of a known defect using the native best match skull, our statistical average skull, and worst match skull was 0.58, 0.74, and 4.4 mm, respectively.

Conclusions:

The ability to statistically average craniofacial surface topography will be a valuable instrument for deriving missing anatomy in complex craniofacial defects and deficiencies as well as in evaluating morphologic results of surgery.
Shared Surgical Decision Making and Youth Resilience Correlates of Satisfaction With Clinical Outcomes
Authors: Kapp-Simon Kathleen A. , Edwards Todd , Ruta Caroline , Bellucci Claudia Crilly , Aspirnall Cassandra L. , Strauss Ronald P. , Topolski Tari D. , Rumsey Nichola J. , Patrick Donald L.
Published: June 2015

The aim of this study was to identify factors associated with youth satisfaction with surgical procedures performed to address oral cleft or craniofacial conditions (CFCs). It was hypothesized that youth mental health, participation in decision making, perceived consequences of living with a CFC, and coping strategies would be associated with satisfaction with past surgeries. A total of 203 youth between the ages of 11 and 18 years (mean age = 14.5, standard deviation = 2.0, 61% male participants, 78% oral cleft) completed a series of questionnaires measuring depression, self-esteem, participation in decision making, condition severity, negative and positive consequences of having a CFC, coping, and satisfaction with past surgeries. Multiple regression analysis using boot-strapping techniques found that youth participation in decision making, youth perception of positive consequences of having a CFC, and coping accounted for 32% of the variance in satisfaction with past surgeries (P < 0.001). Youth age, sex, and assessment of condition severity were not significantly associated with satisfaction with surgical outcome. Depression, self-esteem, and negative consequences of having a CFC were not associated with satisfaction with past surgeries. Youth should be actively involved in the decision for craniofacial surgery. Youth who were more satisfied with their surgical outcomes also viewed themselves as having gained from the experience of living with a CFC. They felt that having a CFC made them stronger people and they believed that they were more accepting of others and more in touch with others’ feelings because of what they had been through.
On enhancing variation detection through pan-genome indexing
Authors: Valenzuela Daniel , Välimäki Niko , Pitkänen Esa , Mäkinen Veli
Published: June 2015

Detection of genomic variants is commonly conducted by aligning a set of reads sequenced from an individual to the reference genome of the species and analyzing the resultingread pileup. Typically, this process finds a subset of variants already reported in databases and additional novel variants characteristic to the sequenced individual. Most of the effort in the literature has been put to the alignment problem on a single reference sequence, although our gathered knowledge on species such as human ispan-genomic: We know most of the common variation in addition to the reference sequence. There have been some efforts to exploitpan-genome indexing, where the most widely adopted approach is to build an index structure on a set of reference sequences containing observed variation combinations.

The enhancement in alignment accuracy when using pan-genome indexing has been demonstrated in experiments, but so far the abovemultiple referencespan-genome indexing approach has not that much been tested on its final goal, that is, in enhancing variation detection. This is the focus of this article: We study a generic approach to add variation detection support on top of the multiple references pan-genomic indexing approach. Namely, we study the read pileup on a multiple alignment of reference genomes, and propose a heaviest path algorithm to extract a new recombined reference sequence. This recombined reference sequence can then be utilized in any standard read alignment and variation detection workflow. We demonstrate that the approach enhances variation detection on realistic data sets.
A laboratory-based Laue X-ray diffraction system for enhanced imaging range and surface grain mapping
Authors: Whitley William , Stock Chris , Huxley Andrew D.
Published: June 2015

Although CCD X-ray detectors can be faster to use, their large-area versions can be much more expensive than similarly sized photographic plate detectors. When indexing X-ray diffraction patterns, large-area detectors can prove very advantageous as they provide more spots, which makes fitting an orientation easier. On the other hand, when looking for single crystals in a polycrystalline sample, the speed of CCD detectors is more useful. A new setup is described here which overcomes some of the limitations of limited-range CCD detectors to make them more useful for indexing, whilst at the same time making it much quicker to find single crystals within a larger polycrystalline structure. This was done by combining a CCD detector with a six-axis goniometer, allowing the compilation of images from different angles into a wide-angled image. Automated scans along the sample were coupled with image processing techniques to produce grain maps, which can then be used to provide a strategy to extract single crystals from a polycrystal.
Quantitative voxel-to-voxel comparison of TriBeam and DCT strontium titanate three-dimensional data sets
Authors: Lenthe William C. , Echlin McLean P. , Trenkle Andreas , Syha Melanie , Gumbsch Peter , Pollock Tresa M.
Published: June 2015

Recently, techniques for the acquisition of three-dimensional tomographic and four-dimensional time-resolved data sets have emerged, allowing for the analysis of mm3 volumes of material with nm-scale resolution. The ability to merge multi-modal data sets acquired via multiple techniques for the quantitative analysis of structure, chemistry and phase information is still a significant challenge. Large three-dimensional data sets have been acquired by time-resolved diffraction contrast tomography (DCT) and a new TriBeam tomography technique with high spatial resolution to address grain growth in strontium titanate. A methodology for combining three-dimensional tomographic data has been developed. Algorithms for the alignment of orientation reference frames, unification of sampling grids and automated grain matching have been integrated, and the resulting merged data set permits the simultaneous analysis of all tomographic data on a voxel-by-voxel and grain-by-grain basis. Quantitative analysis of merged data sets collected using DCT and TriBeam tomography shows that the spatial resolution of the DCT technique is limited near grain boundaries and the sample edge, resolving grains down to 10 µm diameter for the reconstruction method used. While the TriBeam technique allows for higher-resolution analysis of boundary plane location, it is a destructive tomography approach and can only be employed at the conclusion of a four-dimensional experiment.
BINoculars: data reduction and analysis software for two-dimensional detectors in surface X-ray diffraction
Authors: Roobol Sander , Onderwaater Willem , Drnec Jakub , Felici Roberto , Frenken Joost
Published: June 2015

BINoculars is a tool for data reduction and analysis of large sets of surface diffraction data that have been acquired with a two-dimensional X-ray detector. The intensity of each pixel of a two-dimensional detector is projected onto a three-dimensional grid in reciprocal-lattice coordinates using a binning algorithm. This allows for fast acquisition and processing of high-resolution data sets and results in a significant reduction of the size of the data set. The subsequent analysis then proceeds in reciprocal space. It has evolved from the specific needs of the ID03 beamline at the ESRF, but it has a modular design and can be easily adjusted and extended to work with data from other beamlines or from other measurement techniques. This paper covers the design and the underlying methods employed in this software package and explains how BINoculars can be used to improve the workflow of surface X-ray diffraction measurements and analysis.
TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits
Authors: Farabella Irene , Vasishtan Daven , Joseph Agnel Praveen , Pandurangan Arun Prasad , Sahota Harpal , Topf Maya
Published: June 2015

Three-dimensional electron microscopy is currently one of the most promising techniques used to study macromolecular assemblies. Rigid and flexible fitting of atomic models into density maps is often essential to gain further insights into the assemblies they represent. Currently, tools that facilitate the assessment of fitted atomic models and maps are needed. TEMPy (template and electron microscopy comparison using Python) is a toolkit designed for this purpose. The library includes a set of methods to assess density fits in intermediate-to-low resolution maps, both globally and locally. It also provides procedures for single-fit assessment, ensemble generation of fits, clustering, and multiple and consensus scoring, as well as plots and output files for visualization purposes to help the user in analysing rigid and flexible fits. The modular nature of TEMPy helps the integration of scoring and assessment of fits into large pipelines, making it a tool suitable for both novice and expert structural biologists.
Optical design and multi-length-scale scanning spectro-microscopy possibilities at the Nanoscopium beamline of Synchrotron Soleil
Authors: Somogyi Andrea , Medjoubi Kadda , Baranton Gil , Le Roux Vincent , Ribbens Marc , Polack François , Philippot Pascal , Samama Jean-Pierre
Published: June 2015

The Nanoscopium 155 m-long beamline of Synchrotron Soleil is dedicated to scanning hard X-ray nanoprobe techniques. Nanoscopium aims to reach ≤100 nm resolution in the 5–20 keV energy range for routine user experiments. The beamline design tackles the tight stability requirements of such a scanning nanoprobe by creating an overfilled secondary source, implementing all horizontally reflecting main beamline optics, applying high mechanical stability equipment and constructing a dedicated high-stability building envelope. Multi-technique scanning imaging and tomography including X-ray fluorescence spectrometry and spectro-microscopy, absorption, differential phase and dark-field contrasts are implemented at the beamline in order to provide simultaneous information on the elemental distribution, speciation and sample morphology. This paper describes the optical concept and the first measured performance of the Nanoscopium beamline followed by the hierarchical length-scale multi-technique imaging experiments performed with dwell times down to 3 ms per pixel.
Structure determination of KScS2, RbScS2and KLnS2(Ln = Nd, Sm, Tb, Dy, Ho, Er, Tm and Yb) and crystal–chemical discussion
Authors: Havlák Lubomír , Fábry Jan , Henriques Margarida , Dušek Michal
Published: June 2015

The title structures of KScS2(potassium scandium sulfide), RbScS2(rubidium scandium sulfide) and KLnS2[Ln = Nd (potassium neodymium sufide), Sm (potassium samarium sulfide), Tb (potassium terbium sulfide), Dy (potassium dysprosium sulfide), Ho (potassium holmium sulfide), Er (potassium erbium sulfide), Tm (potassium thulium sulfide) and Yb (potassium ytterbium sulfide)] are either newly determined (KScS2, RbScS2and KTbS2) or redetermined. All of them belong to the α-NaFeO2structure type in agreement with the ratio of the ionic radiir3+/r+. KScS2, the member of this structural family with the smallest trivalent cation, is an extreme representative of these structures with rare earth trivalent cations. The title structures are compared with isostructural alkali rare earth sulfides in plots showing the dependence of several relevant parameters on the trivalent cation crystal radius; the parameters thus compared arec,aandc/a, the thicknesses of the S—S layers which contain the respective constituent cations, the sulfur fractional coordinatesz(S2−) and the bond-valence sums.
Crystallographic analysis of theArabidopsis thalianaBAG5–calmodulin protein complex
Authors: Cui Boyang , Fang Shasha , Xing Yangfei , Shen Yuequan , Yang Xue
Published: June 2015

Arabidopsis thalianaBAG5 (AtBAG5) belongs to the plant BAG (Bcl-2-associated athanogene) family that performs diverse functions ranging from growth and development to abiotic stress and senescence. BAG family members can act as nucleotide-exchange factors for heat-shock protein 70 (Hsp70) through binding of their evolutionarily conserved BAG domains to the Hsp70 ATPase domain, and thus may be involved in the regulation of chaperone-mediated protein folding in plants. AtBAG5 is distinguished from other family members by the presence of a unique IQ motif adjacent to the BAG domain; this motif is specific for calmodulin (CaM) binding, indicating a potential role in the plant calcium signalling pathway. To provide a better understanding of the IQ motif-mediated interaction between AtBAG5 and CaM, the two proteins were expressed and purified separately and then co-crystallized together. Diffraction-quality crystals of the complex were grown using the sitting-drop vapour-diffusion technique from a condition consisting of 0.1 MTris–HCl pH 8.5, 2.5 Mammonium sulfate. The crystals belonged to space groupP212121, with unit-cell parametersa= 64.56,b= 74.89,c= 117.09 Å. X-ray diffraction data were recorded to a resolution of 2.5 Å from a single crystal using synchrotron radiation. Assuming the presence of two molecules in the asymmetric unit, a Matthews coefficient of 2.44 Å3 Da−1was calculated, corresponding to a solvent content of approximately 50%.
Synthesis, purification and crystallographic studies of the C-terminal sterol carrier protein type 2 (SCP-2) domain of human hydroxysteroid dehydrogenase-like protein 2
Authors: Cheng Zhong , Li Yao , Sui Chun , Sun Xiaobo , Xie Yong
Published: June 2015

Human hydroxysteroid dehydrogenase-like protein 2 (HSDL2) is a member of the short-chain dehydrogenase/reductase (SDR) subfamily of oxidoreductases and contains an N-terminal catalytic domain and a C-termianl sterol carrier protein type 2 (SCP-2) domain. In this study, the C-terminal SCP-2 domain of human HSDL2, including residues Lys318–Arg416, was produced inEscherichia coli, purified and crystallized. X-ray diffraction data were collected to 2.10 Å resolution. The crystal belonged to the trigonal space groupP3121 (orP3221), with unit-cell parametersa=b= 70.4,c= 60.6 Å, α = β = 90, γ = 120°. Two protein molecules are present in the asymmetric unit, resulting in a Matthews coefficient of 2.16 Å3 Da−1and an approximate solvent content of 43%.
Trace fluorescent labeling for protein crystallization
Authors: Pusey Marc , Barcena Jorge , Morris Michelle , Singhal Anuj , Yuan Qunying , Ng Joseph
Published: June 2015

Fluorescence can be a powerful tool to aid in the crystallization of proteins. In the trace-labeling approach, the protein is covalently derivatized with a high-quantum-yield visible-wavelength fluorescent probe. The final probe concentration typically labels ≤0.20% of the protein molecules, which has been shown to not affect the crystal nucleation or diffraction quality. The labeled protein is then used in a plate-screening experiment in the usual manner. As the most densely packed state of the protein is the crystalline form, then crystals show as the brightest objects in the well under fluorescent illumination. A study has been carried out on the effects of trace fluorescent labeling on the screening results obtained compared with nonlabeled protein, and it was found that considering the stochastic nature of the crystal nucleation process the presence of the probe did not affect the outcomes obtained. Other effects are realised when using fluorescence. Crystals are clearly seen even when buried in precipitate. This approach also finds `hidden' leads, in the form of bright spots, with ∼30% of the leads found being optimized to crystals in a single-pass optimization trial. The use of visible fluorescence also enables the selection of colors that bypass interfering substances, and the screening materials do not have to be UV-transparent.
The structure of nerve growth factor in complex with lysophosphatidylinositol
Authors: Sun Han-Li , Jiang Tao
Published: June 2015

Nerve growth factor (NGF) is an important protein that is involved in a variety of physiological processes in cell survival, differentiation, proliferation and maintenance. The previously reported crystal structure of mouse NGF (mNGF) in complex with lysophosphatidylserine (LysoPS) showed that mNGF can bind LysoPS at its dimeric interface. To expand the understanding of the structural basis for specific lipid recognition by NGF, the crystal structure of mNGF complexed with lysophosphatidylinositol (13:0 LysoPI) was solved. Interestingly, in addition to Lys88, which interacts with the head glycerol group and the phosphate group of LysoPI, as seen in the mNGF–LysoPS structure, two additional residues, Tyr52 and Arg50, were found to assist in lipid binding by forming hydrogen bonds to the inositol moiety of the LysoPI molecule. The results suggest a specific recognition mechanism of inositol group-containing lipids by NGF, which may help in the design of bioactive compounds that can be delivered by NGF.
Expression, purification, crystallization and crystallographic study of theAspergillus terreusaromatic prenyltransferase AtaPT
Authors: Gao Bingquan , Chen Ridao , Liu Xiao , Dai Jungui , Sun Fei
Published: June 2015

Prenylated aromatics are produced by aromatic prenyltransferases during the secondary metabolism of bacteria, fungi and plants. The prenylation of nonprenylated precursors can lead to great chemical diversity and extensive biological properties.Aspergillus terreusaromatic prenyltransferase (AtaPT), which has recently been discovered and characterized, is such an enzyme and is responsible for the prenylation of various aromatic compounds. Here, recombinant AtaPT was overexpressed inEscherichia coli, purified and crystallized. Diffraction data were collected to a resolution of 1.71 Å and the crystal belonged to space groupP21212, with unit-cell parametersa= 96.2,b = 135.8,c= 69.5 Å, α = β = γ = 90°. Analysis of the calculated Matthews coefficient and the self-rotation function suggested that there are two AtaPT molecules in the asymmetric unit.
Towards time-resolved serial crystallography in a microfluidic device
Authors: Pawate Ashtamurthy S. , Šrajer Vukica , Schieferstein Jeremy , Guha Sudipto , Henning Robert , Kosheleva Irina , Schmidt Marius , Ren Zhong , Kenis Paul J. A. , Perry Sarah L.
Published: June 2015

Serial methods for crystallography have the potential to enable dynamic structural studies of protein targets that have been resistant to single-crystal strategies. The use of serial data-collection strategies can circumvent challenges associated with radiation damage and repeated reaction initiation. This work utilizes a microfluidic crystallization platform for the serial time-resolved Laue diffraction analysis of macroscopic crystals of photoactive yellow protein (PYP). Reaction initiation was achievedviapulsed laser illumination, and the resultant electron-density difference maps clearly depict the expected pR1/pRE46Qand pR2/pRCWstates at 10 µs and the pB1intermediate at 1 ms. The strategies presented here have tremendous potential for extension to chemical triggering methods for reaction initiation and for extension to dynamic, multivariable analyses.
Fusion-protein-assisted protein crystallization
Authors: Kobe Bostjan , Ve Thomas , Williams Simon J.
Published: June 2015

Fusion proteins can be used directly in protein crystallization to assist crystallization in at least two different ways. In one approach, the `heterologous fusion-protein approach', the fusion partner can provide additional surface area to promote crystal contact formation. In another approach, the `fusion of interacting proteins approach', protein assemblies can be stabilized by covalently linking the interacting partners. The linker connecting the proteins plays different roles in the two applications: in the first approach a rigid linker is required to reduce conformational heterogeneity; in the second, conversely, a flexible linker is required that allows the native interaction between the fused proteins. The two approaches can also be combined. The recent applications of fusion-protein technology in protein crystallization from the work of our own and other laboratories are briefly reviewed.
Crystal structure of 2-amino-4-phenyl-4H-benzo[h]chromene-3-carbonitrile
Authors: Mohamed Shaaban K. , Horton Peter N. , Akkurt Mehmet , Younes Sabry H. H. , Albayati Mustafa R.
Published: June 2015

In the title compound, C20H14N2O, the plane of the phenyl ring is almost normal to that of the naphthalene ring system, forming a dihedral angle of 83.15 (8)°. The 4H-pyran ring fused with the naphthalene ring system has a flattened boat conformation. In the crystal, molecules are linked by pairs of N—H...N hydrogen bonds, forming inversion dimers with anR22(12) ring motif. The dimers are connected by C—H...π interactions, forming supramolecular chains along [010].
Crystal structure of ethyl 2-(2,4,5-trimethoxyphenyl)quinoline-4-carboxylate
Authors: Shrungesh Kumar T. O. , Naveen S. , Kumara M. N. , Mahadevan K. M. , Lokanath N. K.
Published: June 2015

In the title compound, C21H21NO5, the dihedral angle between the quinoline ring system (r.m.s. deviation = 0.028 Å) and the trimethoxybenzene ring is 43.38 (5)°. The C atoms of the methoxy groups deviate from their attached benzene ring by −0.396 (2), −0.049 (2) and 0.192 (2) Å for theortho-,meta- andpara-substituents, respectively. The pendant ethyl chain is disordered over two orientations in a 0.527 (5):0.473 (5) ratio. A short intramolecular C—H...O contact closes anS(6) ring. In the crystal, inversion dimers linked by pairs of weak C—H...O interactions generateR22(6) loops. The dimers are linked by further C—H...O interactions to generate [1-10] chains.
Crystal structures of 4-chloropyridine-2-carbonitrile and 6-chloropyridine-2-carbonitrile exhibit different intermolecular π-stacking, C—H...Nnitrileand C—H...Npyridineinteractions
Authors: Montgomery Matthew J. , O'Connor Thomas J. , Tanski Joseph M.
Published: June 2015

The two title compounds are isomers of C6H3ClN2containing a pyridine ring, a nitrile group, and a chloro substituent. The molecules of each compound pack together in the solid state with offset face-to-face π-stacking, and intermolecular C—H...Nnitrileand C—H...Npyridineinteractions. 4-Chloropyridine-2-carbonitrile, (I), exhibits pairwise centrosymmetric head-to-head C—H...Nnitrileand C—H...Npyridineinteractions, forming one-dimensional chains, which are π-stacked in an offset face-to-face fashion. The intermolecular packing of the isomeric 6-chloropyridine-2-carbonitrile, (II), which differs only in the position of the chloro substituent on the pyridine ring, exhibits head-to-tail C—H...Nnitrileand C—H...Npyridineinteractions, forming two-dimensional sheets which are π-stacked in an offset face-to-face fashion. In contrast to (I), the offset face-to-face π-stacking in (II) is formed between molecules with alternating orientations of the chloro and nitrile substituents.
Crystal structure of 4-(6-chloro-4-oxo-4H-chromen-3-yl)-2-methylamino-3-nitro-4H,5H-pyrano[3,2-c]chromen-5-one chloroform monosolvate
Authors: Raja Rajamani , Kandhasamy Subramani , Perumal Paramasivam T. , SubbiahPandi A.
Published: June 2015

In the title compound, C23H14Cl4N2O7, the pyran ring has an envelope conformation with the methine C atom as the flap. The chromene rings are almost planar (r.m.s. deviations of 0.027 and 0.018 Å) and their mean planes are inclined to one another by 85.61 (10)°. The mean planes of the pyran ring and the chromene ring fused to it are inclined to one another by 7.41 (13)°. The molecular structure is stabilized by an intramolecular N—H...O hydrogen bond, generating anS(6) ring motif. In the crystal, molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with anR22(12) ring motif. The dimers are linked by pairs of C—H...O hydrogen bonds, enclosingR22(18) ring motifs, forming chains along [010]. Within the chains there are C—H...π interactions. The chains are linkedviaslipped parallel π–π interactions, forming a three-dimensional structure [the shortest inter-centroid distance is 3.7229 (19) Å].
Redetermination of the crystal structure of β-zinc molybdate from single-crystal X-ray diffraction data
Authors: Mtioui-Sghaier Olfa , Mendoza-Meroño Rafael , Ktari Lilia , Dammak Mohamed , García-Granda Santiago
Published: June 2015

The crystal structure of the β-polymorph of ZnMoO4was re-determined on the basis of single-crystal X-ray diffraction data. In comparison with previous powder X-ray diffraction studies [Katikaneani & Arunachalam (2005).Eur. J. Inorg. Chem. pp. 3080–3087; Cavalcanteet al.(2013).Polyhedron,54, 13–25], all atoms were refined with anisotropic displacement parameters, leading to a higher precision with respect to bond lengths and angles. β-ZnMoO4adopts the wolframite structure type and is composed of distorted ZnO6and MoO6octahedra, both with point group symmetry 2. The distortion of the octahedra is reflected by variation of bond lengths and angles from 2.002 (3)–2.274 (4) Å, 80.63 (11)–108.8 (2)° for equatorial and 158.4 (2)– 162.81 (14)° for axial angles (ZnO6), and of 1.769 (3)–2.171 (3) Å, 73.39 (16)–104.7 (2), 150.8 (2)–164.89 (15)° (MoO6), respectively. In the crystal structure, the same type ofMO6octahedra share edges to built up zigzag chains extending parallel to [001]. The two types of chains are condensed by common vertices into a framework structure. The crystal structure can alternatively be described as derived from a distorted hexagonally closed packed arrangement of the O atoms, with Zn and Mo in half of the octahedral voids.