bluuebunny/crossref_metadata_2025 huggingface dataset:
Benefits of thin‐shelled acetabular components for metal‐on‐metal hip resurfacing arthroplasty
Authors: Le Duff Michel J. , Wang Chen‐Ti , Wisk Lauren E. , Takamura Kohtaroh B. , Amstutz Harlan C.
Published: June 2010

The theoretical advantage of using thinner acetabular components in hip resurfacing has not yet been clinically verified. Our purpose was to test the hypothesis of bone conservation and assess the effects of using a thinner acetabular component on hip biomechanics and clinical outcome. We compared the bone conservation, biomechanical results, and functional outcomes between hips in 35 patients who received bilateral metal‐on‐metal resurfacing arthroplasties with acetabular components of 5 mm thickness on one side and 3.5 mm thickness on the other. Acetabular abduction angle and acetabular anteversion were measured using Ein‐Bild‐Röentgen‐Analysis software. Medial acetabular wall thickness and position of the hip center of rotation were measured using Image J software. The change in position of the hip center of rotation was minimal and did not reach significance. Thin‐shelled components showed greater bone conservation on the acetabular side measured by an increase in the medial acetabular wall thickness. Bone conservation on the femoral side was achieved as well with thin shells. Range of motion, pain scores, and complication rates were comparable. No appreciable difference was found in bone‐cup radiographic appearance between the two types of components. These data suggest that patients can experience good clinical outcomes for resurfacing with either thin or thick‐shelled acetabular components. However, thin‐shelled components preserve acetabular bone stock and allow the use of a larger femoral component. The use of thinner acetabular components is an improvement in bone conservation for a hip resurfacing design. © 2010 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 28:1665–1670, 2010
The role of core needle biopsy in the diagnosis of suspected soft tissue tumours
Authors: Strauss D.C. , Qureshi Y.A. , Hayes A.J. , Thway K. , Fisher C. , Thomas J.M.
Published: June 2010

Background

Controversy surrounds the biopsy method of choice for the histological diagnosis of soft tissue sarcoma. The objective of this study was to evaluate the diagnostic accuracy of core needle biopsy (CNB) in patients referred with the suspicion of a soft tissue sarcoma.

Methodology

Previously undiagnosed patients (n = 530) with a suspected soft tissue tumour (STT) who underwent CNB at initial presentation were identified. Specific end‐points were the ability to differentiate benign from malignant tumours, soft tissue from non‐STT, and for sarcomas to define subtype and grade.

Results

Of the 530 patients, 426 patients (80.4%) with soft tissue tumours were identified, of which 225 (52.8%) were malignant and 201 (47.2%) benign. In the remaining 104 patients, tumours masquerading as STT were diagnosed. CNB could differentiate soft tissue sarcomas from benign soft tissue tumours with an accuracy of 97.6%. High grade were differentiated from low grade sarcomas with an accuracy of 86.3%. Tumour subtype was accurately assigned in 89.5% of benign tumours and 88.0% of sarcomas.

Conclusion

CNB is simple, safe and can accurately diagnose benign and malignant soft tissue tumours. It can reliably identify other tumours masquerading as sarcoma. CNB should be the method of choice to obtain a histological diagnosis in suspected STT. J. Surg. Oncol. 2010;102:523–529. © 2010 Wiley‐Liss, Inc.
Clinicopathologic features and prognostic factors in alpha‐fetoprotein‐producing gastric cancers: Analysis of 104 cases
Authors: Liu Xiaowen , Cheng Yufan , Sheng Weiqi , Lu Hongfen , Xu Yu , Long Ziwen , Zhu Huiyan , Wang Yanong
Published: June 2010

Background and Objectives

There were no comprehensive studies on the clinicopathologic features and prognosis of alpha‐protein‐producing gastric cancer. The aim of this study was to elucidate the clinicopathologic characteristics and prognostic factors of alpha‐fetoprotein (AFP)‐producing gastric cancer.

Methods

Among 4,426 gastric cancer patients receiving surgery in the Cancer Hospital of Fudan University from 1996 to 2007, there were 111 patients with elevated serum level of AFP preoperatively after excluding chronic hepatitis, hepatocirrhosis, and hepatocellular carcinoma. Primary lesions of 104 patients were stained positively for AFP. The clinicopathologic characteristics and prognostic factors of AFP‐producing gastric cancer were analyzed. Additionally, 208 stage‐matched AFP‐negative gastric cancer patients were selected as control.

Results

There was a significantly higher incidence of vascular invasion, lymph node metastasis, and liver metastasis in AFP‐positive group than in the negative group. The overall 5‐year survival rates of AFP‐positive and negative groups were 28% and 38%, respectively. The AFP‐positive group had a significantly poorer survival in comparison to the stage‐matched negative group. The independent prognostic factors of AFP‐positive group included liver metastasis and pathological stage.

Conclusions

AFP‐positive gastric cancer had more aggressive behavior than that of AFP‐negative gastric cancer. In addition to surgery, multimodal therapy should be considered. J. Surg. Oncol. 2010;102:249–255. © 2010 Wiley‐Liss, Inc.
Inhibition of cytosolic chaperonin CCTζ‐1 expression depletes proliferation of colorectal carcinoma in vitro
Authors: Qian‐Lin Zhu , Ting‐Feng Wang , Qi‐Feng Cao , Min‐Hua Zheng , Ai‐Guo Lu
Published: June 2010

Background

It is important to identify the behavior of colorectal cancer (CRC) individually, so more accurate laboratory index is urgently demanded. Chaperonin are key molecules in tumor cell cycle. Our study aims at revealing the expression and correlation of chaperonin containing TCP1 complex 6A (CCTζ‐1) in CRC.

Methods

Fifty‐eight patients with CRC admitted from 2005 to 2008 were selected. CCTζ‐1 expression in cell, tumor, and non‐tumor colorectal tissues was detected by Western blot, and their protein was localized by immunohistochemical stain. After HCT116 cells were transfected with CCTζ‐1 siRNA, real‐time PCR, and Western blot were used to examine gene expression. Cell multiplication and apoptosis were examined by Cell Counting Kit‐8 and Annexin V kit.

Results

CCTζ‐1 ptotein expression was detected in 51 of 58 (87.9%) CRC specimens, which was much higher than those in normal mucosa (P < 0.01), and it was correlated with tumor invasion (P < 0.01) and tumor size (P < 0.05). The levels of CCTζ‐1 mRNA and protein were inhibited by CCTζ‐1 siRNA in HCT116 cells transfected with CCTζ‐1 siRNA, which resulted in growth arrest but not apoptosis.

Conclusion

CCTζ‐1 could be a new prognostic marker for CRC and involve in tumorigenesis. CCTζ‐1 inhibition in vivo might therefore become a new therapy for CRC. J. Surg. Oncol. 2010;102:419–423. © 2010 Wiley‐Liss, Inc.
Predictors of microvascular invasion before hepatectomy for hepatocellular carcinoma
Authors: Kaibori Masaki , Ishizaki Morihiko , Matsui Kosuke , Kwon A‐Hon
Published: June 2010

Background and Objectives

Microvascular invasion (MVI) is difficult to detect before resection of hepatocellular carcinoma (HCC).

Methods

Clinicopathological and outcome data were retrospectively compared between 213 HCC patients with MVI and 221 patients without MVI who underwent hepatectomy.

Results

MVI risk was selected as an independent prognostic indicator for both disease‐free and overall survival in our 434 HCC patients. Univariate and multivariate analyses showed that an age under 65 years, a protein induced by vitamin K absence/antagonism II (PIVKA‐II) level ≥200 mAU/ml, a preoperative tumor size ≥5.0 cm, and poorly differentiated carcinoma were independent predictors of MVI. When age, PIVKA‐II level, and tumor size (data available before surgery) were scored as a combined index, the total score demonstrated a significant correlation with the extent of vascular invasion and with survival after hepatic resection.

Conclusions

An age under 65 years, increase of PIVKA‐II, and larger tumor size were preoperative predictors of MVI in HCC patients undergoing potentially curative resection. Our combined score based on the age, serum PIVKA‐II, and preoperative tumor size is a reliable predictor of MVI and survival in patients with HCC. J. Surg. Oncol. 2010;102:462–468. © 2010 Wiley‐Liss, Inc.
Earthquake impact in a remote South Asian population: Psychosocial factors and posttraumatic symptoms
Authors: Ahmad Samoon , Feder Adriana , Lee Elisa J. , Wang Yanping , Southwick Steven M. , Schlackman Erica , Buchholz Katherine , Alonso Angelique , Charney Dennis S.
Published: June 2010

Although previous studies have documented the psychological impact of earthquakes, less is known about potentially protective characteristics associated with healthier outcomes. In the present study, 2 samples of survivors were recruited from remote villages in Northwestern Pakistan, 7 and 19 months after the devastating October 2005 earthquake. Female gender, lower education, and closer proximity to the epicenter predicted significantly higher posttraumatic symptom levels. After adjusting for demographic characteristics, distance from the epicenter, and death of close relatives, higher dispositional optimism and higher scores on the Connor‐Davidson Resilience Scale were significantly associated with lower symptom levels. The authors' findings in a previously unstudied population suggest that certain potentially protective mechanisms, such as optimism, may be universal regardless of culture of origin.
Histology of the healing tympanic membrane following perforation in rats
Authors: Santa Maria Peter Luke , Redmond Sharon Leanne , Atlas Marcus David , Ghassemifar Reza
Published: June 2010

Objectives/Hypothesis:

The aim of this study was to provide a detailed cytological account on the healing tympanic membrane (TM) over 14 days and to complement existing research into TM wound healing.

Study Design:

The study is a prospective cohort study of 19 male Sprague‐Dawley (Rattus norvegicus) rats.

Methods:

Rat TMs were perforated using a sterile needle and sacrificed at time points during the 14 days following perforation.

Results:

The healing of the TM resembles cutaneous wound healing except that the TM is unique in the lack of a supportive matrix beneath the regenerating epithelia. This prevents the influx of reparative cells and nutrients and the in growth of the usual fibroblastic reaction.

Conclusions:

TM wound healing contrasts with cutaneous wound healing in that keratinocytes are the first cells to close the wound and not the last. A keratin scaffold may not be important in the healing process. The malleus plays a crucial role in the healing of the TM and is the site of significant mitotic activity during the healing process. Migration across layers of the TM appears to account for the closure of the perforation. Laryngoscope, 2010
Stable overexpression of Pregnane X receptor in HepG2 cells increases its potential for bioartificial liver application
Authors: Nibourg Geert A. A. , Huisman Maarten T. , van der Hoeven Tessa V. , van Gulik Thomas M. , Chamuleau Robert A. F. M. , Hoekstra Ruurdtje
Published: June 2010

To bridge patients with acute liver failure to transplantation or liver regeneration, a bioartificial liver (BAL) is urgently needed. A BAL consists of an extracorporeal bioreactor loaded with a bioactive mass that would preferably be of human origin and display high hepatic functionality, including detoxification. The human hepatoma cell line HepG2 exhibits many hepatic functions, but its detoxification function is low. In this study, we investigated whether stable overexpression of pregnane X receptor (PXR), a master regulator of diverse detoxification functions in the liver [eg, cytochrome P450 3A (CYP3A) activity], would increase the potential of HepG2 for BAL application. Stable overexpression was achieved by lentiviral expression of the human PXR gene, which yielded cell line cBAL119. In monolayer cultures of cBAL119 cells, PXR transcript levels increased 29-fold versus HepG2 cells. Upon activation of PXR by rifampicin, the messenger RNA levels of CYP3A4, CYP3A5, and CYP3A7 increased 49- to 213-fold versus HepG2 cells. According to reporter gene assays with different inducers, the highest increase in CYP3A4 promoter activity (131-fold) was observed upon induction with rifampicin. Inside BALs, the proliferation rates, as measured by the DNA content, were comparable between the 2 cell lines. The rate of testosterone 6β-hydroxylation, a measure of CYP3A function inside BALs, increased 4-fold in cBAL119 BALs versus HepG2 BALs. Other functions, such as apolipoprotein A1 synthesis, urea synthesis, glucose consumption, and lactate production, remained unchanged or increased. Thus, stable PXR overexpression markedly increases the potential of HepG2 for BAL application. Liver Transpl 16:1075-1085, 2010. © 2010 AASLD.
Marketing: Too important to be left to the marketing people
Authors: Trout Jack
Published: June 2010

Jack Trout is a longtime powerhouse in the world of marketing (he coauthored the marketing classic Positioning with Al Ries). The key to surviving in these difficult times, he says, “is not to stare at the balance sheet but simply to know where you must go to find success in a market. That's because no one can follow you (the board, your managers, your employees) if you don't know where you're headed.” How do you find the proper direction? Trout outlines a four‐step process to pursue in forging the way ahead.
Strategies for growth in hard times
Authors: Kanwar Onkar S.
Published: June 2010

Apollo Tyres, headquartered in India, has gone through multiple sets of difficult times during its short history, including near‐bankruptcy. Onkar S. Kanwar, chairman of Apollo Tyres, offers key lessons for all companies on how his company dealt with setbacks and challenges to become India's leading automotive tire manufacturer, with operations on three continents.
Food processing increases casein resistance to simulated infant digestion
Authors: Dupont Didier , Mandalari Giuseppina , Mollé Daniel , Jardin Julien , Rolet‐Répécaud Odile , Duboz Gabriel , Léonil Joëlle , Mills Clare E. N. , Mackie Alan R.
Published: June 2010

The objective of this study was to determine whether processing could modify the resistance of casein (CN) to digestion in infants. A range of different dairy matrices was manufactured from raw milk in a pilot plant and subjected to in vitro digestion using an infant gut model. Digestion products were identified using MS and immunochemical techniques. Results obtained showed that CNs were able to resist digestion, particularly κ‐ and αs2‐CN. Resistant areas were identified and corresponded to fragments hydrophobic at pH 3.0 (gastric conditions) and/or carrying post‐translational modifications (phosphorylation and glycosylation). Milk processing led to differences in peptide patterns and heat treatment of milk tended to increase the number of peptides found in digested samples. This highlights the likely impact of milk processing on the allergenic potential of CNs.
Anti‐invasion effects of 6‐shogaol and 6‐gingerol, two active components in ginger, on human hepatocarcinoma cells
Authors: Weng Chia‐Jui , Wu Cheng‐Feng , Huang Hsiao‐Wen , Ho Chi‐Tang , Yen Gow‐Chin
Published: June 2010

Scope: Hepatocellular carcinoma is the most common type of liver cancer and is highly metastatic. Metastasis is considered to be the major cause of death in cancer patients. Ginger is a natural dietary rhizome with anti‐oxidative, anti‐inflammatory, and anti‐carcinogenic activities. The aims of this study were to evaluate the anti‐invasion activity of 6‐shogaol and 6‐gingerol, two compounds found in ginger, on hepatoma cells. Methods and results: The migratory and invasive abilities of phorbol 12‐myristate 13‐acetate (PMA)‐treated HepG2 and PMA‐untreated Hep3B cells were both reduced in a dose‐dependent manner by treatment with 6‐shogaol and 6‐gingerol. Upon incubation of PMA‐treated HepG2 cells and PMA‐untreated Hep3B cells with 6‐shogaol and 6‐gingerol, matrix metalloproteinase (MMP)‐9 activity decreased, whereas the expression of tissue inhibitor metalloproteinase protein (TIMP)‐1 increased in both cell types. Additionally, urokinase‐type plasminogen activator activity was dose‐dependently decreased in Hep3B cells after incubation with 6‐shogaol for 24 h. Analysis with semi‐quantitative reverse transcription‐PCR showed that the regulation of MMP‐9 by 6‐shogaol and 6‐gingerol and the regulation of TIMP‐1 by 6‐shogaol in Hep3B cells may on the transcriptional level. Conclusions: These results suggest that 6‐shogaol and 6‐gingerol might both exert anti‐invasive activity against hepatoma cells through regulation of MMP‐9 and TIMP‐1 and that 6‐shogaol could further regulate urokinase‐type plasminogen activity.
Shaping and timing gradient pulses to reduce MRI acoustic noise
Authors: Segbers Marcel , Rizzo Sierra Carlos V. , Duifhuis Hendrikus , Hoogduin Johannes M.
Published: June 2010

A method to reduce the acoustic noise generated by gradient systems in MRI has been recently proposed; such a method is based on the linear response theory. Since the physical cause of MRI acoustic noise is the time derivative of the gradient current, a common trapezoid current shape produces an acoustic gradient coil response mainly during the rising and falling edge. In the falling edge, the coil acoustic response presents a 180° phase difference compared to the rising edge. Therefore, by varying the width of the trapezoid and keeping the ramps constant, it is possible to suppress one selected frequency and its higher harmonics. This value is matched to one of the prominent resonance frequencies of the gradient coil system. The idea of cancelling a single frequency is extended to a second frequency, using two successive trapezoid‐shaped pulses presented at a selected interval. Overall sound pressure level reduction of 6 and 10 dB is found for the two trapezoid shapes and a single pulse shape, respectively. The acoustically optimized pulse shape proposed is additionally tested in a simulated echo planar imaging readout train, obtaining a sound pressure level reduction of 12 dB for the best case. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Nurse burnout and quality of care: Cross‐national investigation in six countries
Authors: Poghosyan Lusine , Clarke Sean P. , Finlayson Mary , Aiken Linda H.
Published: June 2010

We explored the relationship between nurse burnout and ratings of quality of care in 53,846 nurses from six countries. In this secondary analysis, we used data from the International Hospital Outcomes Study; data were collected from 1998 to 2005. The Maslach Burnout Inventory and a single‐item reflecting nurse‐rated quality of care were used in multiple logistic regression modeling to investigate the association between nurse burnout and nurse‐rated quality of care. Across countries, higher levels of burnout were associated with lower ratings of the quality of care independent of nurses' ratings of practice environments. These findings suggest that reducing nurse burnout may be an effective strategy for improving nurse‐rated quality of care in hospitals. © 2010 Wiley Periodicals, Inc. Res Nurs Health 33:288–298, 2010
The beginning breastfeeding survey: Measuring mothers' perceptions of breastfeeding effectiveness during the postpartum hospitalization
Authors: Mulder Pamela J. , Johnson Teresa S.
Published: June 2010

No current breastfeeding assessment tool assesses the mother's perception of breastfeeding effectiveness during the early postpartum. Psychometric analysis of a new tool, the Beginning Breastfeeding Survey (BBS), in a multi‐racial sample of 131 women revealed a coefficient alpha of .90. Factor analysis yielded three factors, (a) Maternal Breastfeeding Competence and Emotional Satisfaction, (b) Maternal Discomfort and Anxiety, and (c) Infant Breastfeeding Skill and Emotional Satisfaction. The BBS demonstrated discriminant validity in known group analyses and convergent validity with breastfeeding self‐efficacy and postpartum fatigue. Future research will focus on improving the internal consistency reliability of the BBS and examining its ability to identify women at risk for breastfeeding problems during the postpartum hospitalization. © 2010 Wiley Periodicals, Inc. Res Nurs Health 33:329–344, 2010
Circularly permuted monomeric red fluorescent proteins with new termini in the β‐sheet
Authors: Carlson Haley J. , Cotton Darrel W. , Campbell Robert E.
Published: June 2010

Circularly permuted fluorescent proteins (FPs) have a growing number of uses in live cell fluorescence biosensing applications. Most notably, they enable the construction of single fluorescent protein‐based biosensors for Ca2+ and other analytes of interest. Circularly permuted FPs are also of great utility in the optimization of fluorescence resonance energy transfer (FRET)‐based biosensors by providing a means for varying the critical dipole–dipole orientation. We have previously reported on our efforts to create circularly permuted variants of a monomeric red FP (RFP) known as mCherry. In our previous work, we had identified six distinct locations within mCherry that tolerated the insertion of a short peptide sequence. Creation of circularly permuted variants with new termini at the locations corresponding to the sites of insertion led to the discovery of three permuted variants that retained no more than 18% of the brightness of mCherry. We now report the extensive directed evolution of the variant with new termini at position 193 of the protein sequence for improved fluorescent brightness. The resulting variant, known as cp193g7, has 61% of the intrinsic brightness of mCherry and was found to be highly tolerant of circular permutation at other locations within the sequence. We have exploited this property to engineer an expanded series of circularly permuted variants with new termini located along the length of the 10th β‐strand of mCherry. These new variants may ultimately prove useful for the creation of single FP‐based Ca2+ biosensors.
Crystal structures of the apo and ATP bound Mycobacterium tuberculosis nitrogen regulatory PII protein
Authors: Shetty Nishant D. , Reddy Manchi C. M. , Palaninathan Satheesh K. , Owen Joshua L. , Sacchettini James C.
Published: June 2010

PII constitutes a family of signal transduction proteins that act as nitrogen sensors in microorganisms and plants. Mycobacterium tuberculosis (Mtb) has a single homologue of PII whose precise role has as yet not been explored. We have solved the crystal structures of the Mtb PII protein in its apo and ATP bound forms to 1.4 and 2.4 Å resolutions, respectively. The protein forms a trimeric assembly in the crystal lattice and folds similarly to the other PII family proteins. The Mtb PII:ATP binary complex structure reveals three ATP molecules per trimer, each bound between the base of the T‐loop of one subunit and the C‐loop of the neighboring subunit. In contrast to the apo structure, at least one subunit of the binary complex structure contains a completely ordered T‐loop indicating that ATP binding plays a role in orienting this loop region towards target proteins like the ammonium transporter, AmtB. Arg38 of the T‐loop makes direct contact with the γ‐phosphate of the ATP molecule replacing the Mg2+ position seen in the Methanococcus jannaschii GlnK1 structure. The C‐loop of a neighboring subunit encloses the other side of the ATP molecule, placing the GlnK specific C‐terminal 310 helix in the vicinity. Homology modeling studies with the E. coli GlnK:AmtB complex reveal that Mtb PII could form a complex similar to the complex in E. coli. The structural conservation and operon organization suggests that the Mtb PII gene encodes for a GlnK protein and might play a key role in the nitrogen regulatory pathway.
Tissue expression of IL16 in prostate cancer and its association with recurrence after radical prostatectomy
Authors: Compérat Eva , Rouprêt Morgan , Drouin Sarah J. , Camparo Philippe , Bitker Marc‐Olivier , Houlgatte Alain , Cancel‐Tassin Géraldine , Cussenot Olivier
Published: June 2010

BACKGROUND

Genetic polymorphism located within the IL16 gene has been reported to be associated with aggressive prostate cancer (PCa). Our aim was to establish whether the tissue expression of IL16 is a prognostic factor of survival in PCa.

METHODS

The files of patients who underwent radical prostatectomy (RP) between 1995 and 2001 were reviewed. The cases were selected and classified according to the D'Amico classification for risk of recurrence (intermediate or high). The value of IL16 and its receptor CCR5 (chemokine (C‐C motif) receptor 5) expression levels were determined as witness of aggressiveness patterns and markers of biological relapse in patients with PCa treated by RP. A tissue microarray of 304 cases was constructed. IL16 and CCR5 expression levels were characterized by immunohistochemistry.

RESULTS

IL16 expression was correlated with high Gleason score (i.e., >7) (P < 0.01). It was not significant for CCR5. IL16 and CCR5 were not associated with prostate‐specific antigen (PSA) or capsular extension of the disease. The accurate prediction of disease outcome, using stratification of cases, according to negative margins and D'Amico classification was significantly enhanced by status of IL16 expression (P ≤ 0.01). In univariate analyses, Gleason score, PSA level, stage and loss of IL16 expression were related to better biological‐free survival (P < 0.05) but not CCR5. In a multivariate analysis, IL16 expression, Gleason score, and tumor stage were independent factors for biochemical‐free survival (P = 0.001).

CONCLUSIONS

IL16 appears to be a useful prognostic factor in PCa. Its expression in PCa tissue was correlated to tumor aggressiveness and biochemical relapse of the disease. Prostate 70: 1622–1627, 2010. © 2010 Wiley‐Liss, Inc.
Similarity of cytochrome c oxidases in different organisms
Authors: Popovic D. M. , Leontyev I. V. , Beech D. G. , Stuchebrukhov A. A.
Published: June 2010

Most of biological oxygen reduction is catalyzed by the heme‐copper oxygen reductases. These enzymes are redox‐driven proton pumps that take part in generating the proton gradient in both prokaryotes and mitochondria that drives synthesis of ATP. The enzymes have been divided into three evolutionarily‐related groups: the A‐, B‐, and C‐families. Recent comparative studies suggest that all oxygen reductases perform the same chemistry for oxygen reduction and comprise the same essential elements of the proton pumping mechanism, such as the proton loading and kinetic gating sites, which, however, appear to be different in different families. All species of the A‐family, however, demonstrate remarkable similarity of the central processing unit of the enzyme, as revealed by their recent crystal structures. Here we demonstrate that cytochrome c oxidases (CcO) of such diverse organisms as a mammal (bovine heart mitochondrial CcO), photosynthetic bacteria (Rhodobacter sphaeroides CcO), and soil bacteria (Paracoccus denitrificans CcO) are not only structurally similar, but almost identical in microscopic electrostatics and thermodynamics properties of their key amino‐acids. By using pKa calculations of some of the key residues of the catalytic site, D‐ and K‐ proton input, and putative proton output channels of these three different enzymes, we demonstrate that the microscopic properties of key residues are almost identical, which strongly suggests the same mechanism in these species. The quantitative precision with which the microscopic physical properties of these enzymes have remained constant despite different evolutionary routes undertaken is striking. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Rosetta in CAPRI rounds 13–19
Authors: Fleishman Sarel J. , Corn Jacob E. , Strauch Eva M. , Whitehead Tim A. , Andre Ingemar , Thompson James , Havranek James J. , Das Rhiju , Bradley Philip , Baker David
Published: June 2010

Modeling the conformational changes that occur on binding of macromolecules is an unsolved challenge. In previous rounds of the Critical Assessment of PRediction of Interactions (CAPRI), it was demonstrated that the Rosetta approach to macromolecular modeling could capture side chain conformational changes on binding with high accuracy. In rounds 13–19 we tested the ability of various backbone remodeling strategies to capture the main‐chain conformational changes observed during binding events. These approaches span a wide range of backbone motions, from limited refinement of loops to relieve clashes in homologous docking, through extensive remodeling of loop segments, to large‐scale remodeling of RNA. Although the results are encouraging, major improvements in sampling and energy evaluation are clearly required for consistent high accuracy modeling. Analysis of our failures in the CAPRI challenges suggest that conformational sampling at the termini of exposed beta strands is a particularly pressing area for improvement. Proteins 2010. © Wiley‐Liss, Inc.
On the pH‐optimum of activity and stability of proteins
Authors: Talley Kemper , Alexov Emil
Published: June 2010

Biological macromolecules evolved to perform their function in specific cellular environment (subcellular compartments or tissues); therefore, they should be adapted to the biophysical characteristics of the corresponding environment, one of them being the characteristic pH. Many macromolecular properties are pH dependent, such as activity and stability. However, only activity is biologically important, while stability may not be crucial for the corresponding reaction. Here, we show that the pH‐optimum of activity (the pH of maximal activity) is correlated with the pH‐optimum of stability (the pH of maximal stability) on a set of 310 proteins with available experimental data. We speculate that such a correlation is needed to allow the corresponding macromolecules to tolerate small pH fluctuations that are inevitable with cellular function. Our findings rationalize the efforts of correlating the pH of maximal stability and the characteristic pH of subcellular compartments, as only pH of activity is subject of evolutionary pressure. In addition, our analysis confirmed the previous observation that pH‐optimum of activity and stability are not correlated with the isoelectric point, pI, or with the optimal temperature. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Zero‐width resonances and exceptional points in molecular photodissociation
Authors: Lefebvre Roland , Atabek Osman
Published: June 2010

In the Hamiltonian describing the interaction of a molecule with a continuous laser field, the wavelength and the intensity of the field are two external parameters which can be varied at will, within realistic limits. Floquet formalism provides complex eigenenergies with an imaginary part giving the photodissociation rate. Two interesting features emerge from this treatment. For some specific laser intensities, the imaginary part can vanish. This means that Zero‐Width Resonances can be produced. It is also possible to choose the laser parameters to provoke the coalescence of two resonances (complex eigenenergies and wavefunctions) of the wave equation. Such points in the parameter plane are called exceptional and have been studied in many areas of physics. The existence of Zero‐Width Resonances and of Exceptional Points has important consequences which are described in the article. Advantage can be taken of them in laser control strategies dealing with vibrational purification or transfer, with the ultimate goal of molecular cooling. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
The electronic terms of the finite‐length nanotubes, generated by edge states: A CASSCF study
Authors: Pavlov Mikhail , Ermilov Alexander
Published: June 2010

Low‐lying electronic terms of the hydrocarbons [C7]q (q = 1,3…9) were calculated within CASSCF approach. The [C7]q are H‐terminated finite fragment of zigzag carbon nanotube (7,0) containing q cyclacene units. Each [C7]q with odd q has D7h point symmetry. All systems [Cn]q with arbitrary n and q have a specific set of the one‐electron states characterized by the exponential decay along the cylinder axis that has been estimated within the Huckel model. These MOs are localized near bases of the cylinder and they are frontier in all systems [Cn]q. By hypothesis, the low‐lying electronic terms of the hydrocarbons [C7]q (q = 1,3…9) are defined by four quasi‐degenerate MOs e3′, e3″, which were included in the active space CASSCF. Low‐lying electronic terms possess tier structure and systems with various q have the same order of states. The distance between tiers tends to asymptotic limit with increasing q. In this case, states in each tier become quasi‐degenerate. The lowest tier consists of close set of states 1A, 3A, 5A, and each is characterized by single occupation of the localized MOs. Ground state of [C7]q is singlet; values of splitting are well described by Heisenberg hamiltonaian. The calculation results can be interpreted as reducing interaction of states localized on opposite cylinder bases with increasing fragment length. According to CASSCF, this interaction reduces exponentially in exact accordance with the similar characteristics of the localized MOs. There is a reason to believe that the value of splitting decreases less rapidly with increasing q if level of calculation is improved. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
A 2D spinless version of Dirac's equation written in a noninertial frame of reference
Authors: Nascimento D. L. , Fonseca A. L. A.
Published: June 2010

In this article, we present a quantized classical‐like wave equation. It is obtained by considering the equivalence between the Hamilton‐Jacobi eq. (which belongs to the usual manifold \input amssym ${\Bbb R^{3}} \otimes {\Bbb R} $ of General Relativity), with our two spinor versions of the Dirac eq. (which belongs to the associated complex manifold \input amssym ${\Bbb C}\otimes {\Bbb C} $). In which the electron is considered as a particle‐like entity, instead of the usual wave‐like interpretation of standard Quantum Mechanics. We also consider the transformation properties between the two manifolds through the corresponding groups O(3,1) and SU(2), but we assume a flat Minkowsky space as the background space. We made an illustrative application to the rather standard problem of the hydrogen and helium atoms. We propose a variational extension of the approach, through a Hylleraas‐like computational method, to take into account a many electron problem too futurely. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Stagnation graphs and topological models of magnetic‐field induced electron current density for some small molecules in connection with their magnetic symmetry
Authors: Pelloni Stefano , Lazzeretti Paolo
Published: June 2010

Spatial models of magnetic‐field induced electronic currents have been constructed for a series of small molecules of different point group symmetry via stagnation graphs and current density maps. These tools provide fundamental help for rationalization of magnetic response properties, such as magnetizability and nuclear magnetic shielding. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Crystal and electronic structure of the room temperature organometallic ferrimagnet V(TCNE)2. Analysis of numerical DoS and magnetic properties as related to orbital and spin‐Hamiltonian models
Authors: Tchougréeff Andrei L. , Dronskowski Richard
Published: June 2010

We present a detailed analysis of the results of our numerical study of the crystal and electronic structure of the room temperature organometallic ferrimagnet of general composition V(TCNE)x with x ≈ 2. The results of the LSDA +U study show that the experimentally determined structure complies with the magnetic measurements and thus can serve as a prototype structure for the entire family of the M(TCNE)2 organometallic magnets. The results of the numerical study and of the magnetic experiments are interpreted using a spin‐wave treatment of the model Hamiltonians proposed here. This allowed us to obtain estimates of the critical temperature in three‐ and two‐dimensional regimes and to give an explanation of the differences in behavior of probably isostructural V(TCNE)2 and Fe(TCNE)2 species. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Computational insights into the photochemical step of the reaction catalyzed by protochlorophylide oxidoreductase
Authors: Silva Pedro J. , Ramos Maria João
Published: June 2010

The light‐dependent enzyme protochlorophyllide oxidoreductase (EC:1.3.1.33) catalyzes the conversion of protochlorophyllide (PChlide) into chlorophyllide during chlorophyll synthesis. The reaction has been proposed to proceed through light‐induced weakening of the C17–C18 double bond in PChlide, which then facilitates hydride transfer from a NADPH cosubstrate molecule. We have performed DFT and TDDFT computations on the reaction mechanism of this interesting enzyme. The results show that whereas in the ground state the reaction is strongly endergonic and has a very high activation free energy (38 kcal/mol), the first four excited states (corresponding to excitations within the conjugated porphyrin π‐system) afford much lower activation free energies (<25 kcal/mol) and spontaneous (or only slightly endergonic) reaction paths. The sharp shape of the potential energy surface along the reaction coordinate in these excited states allows hydrogen tunneling to occur efficiently on the first few excited state surface, lowering the barrier to values closer to experiment, in agreement with recent suggestions. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Interaction of the Mn2+, Co2+, Ni2+, and Zn2+ with prion protein HGGGW pentapeptide model
Authors: Marino Tiziana , Russo Nino , Toscano Marirosa
Published: June 2010

The interaction between the HGGGW model pentapeptide of octapeptide domain of the prion protein and the metal ions Mn2+, Co2+, Ni2+, and Zn2+ was studied at DFT level. For every metal ion considered four complexes with different metal coordination modes were analyzed. The geometry optimizations were performed at PW91PW91 level. Other five exchange‐correlation (XC) potentials were used to verify if the energetic parameters can be affected by the choice of the XC functional. Results showed that the metal ion affinity for the considered metal ions follows the trend: Ni2+ > Cu2+ > Co2+ > Zn2+ > Mn2+, irrespective to the used XC functional. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Magnetic interactions in Ca3Fe2Ge3O12 and Ca3Cr2Ge3O12 garnets. An ab initio all‐electron quantum mechanical simulation
Authors: Meyer A. , Perger W. F. , Demichelis R. , Civalleri B. , Dovesi R.
Published: June 2010

The ground state electronic structure in various magnetic phases of two Ge garnets (80 atoms in the primitive cell; cubic symmetry), Ca3Fe2Ge3O12 and Ca3Cr2Ge3O12, has been investigated with the periodic ab initio CRYSTAL code by adopting an all‐electron Gaussian‐type basis set and two hybrid functionals, namely B3LYP and PBE0, which contain a fraction of exact Hartree–Fock exchange. The evaluation of the exchange coupling constants among first (J1a, and J1b: there are two different kinds of neighbors at the same distance), second (J2), and third (J3) neighbors, separated by about 5.3, 6.1, and 8.7 Å, respectively, requires calculations involving the 160 atoms conventional cell. The Ji values turn out to be in qualitative agreement with experimental data. As a consequence of the different J1a to J1b ratios, and of the opposite sign of J2, two different magnetic ground states are found for the Cr and Fe compounds, in agreement with experimental observations. The mechanism for the stabilization of the magnetic states is discussed in the context of the Anderson theory of superexchange by evaluating the kinetic energy gain in the magnetic states and examining spin density maps and profiles. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Characterization of phenolic compounds in Helichrysum melaleucum by high‐performance liquid chromatography with on‐line ultraviolet and mass spectrometry detection
Authors: Gouveia Sandra C. , Castilho Paula C.
Published: June 2010

Helicrysum melaleucum is a medicinal plant traditionally used in the islands of the Macaronesia region for the treatment of respiratory diseases. In this work, the phenolic compounds of Helicrysum melaleucum plants collected in different geographical locations of Madeira Island and their morphological parts (total aerial parts, leaves, flowers and stems) were extracted and analyzed separately by high‐performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC‐DAD/ESI‐MSn). A total of 68 compounds were characterized based mainly on their UV and mass spectra. These included derivatives of O‐glycosylated flavonoids (flavonol and flavones type), quinic acid, caffeic acid, lignans and polyphenols. The flowers were found to be the morphological part with higher variety of phenolic compounds. The large differences in the phenolic composition of plants collected from different geographical locations allowed the identification of a few components, such as pinoresinol and methoxylated flavone derivatives, likely to be useful as geographical markers. Also, these results promote further comparison of the bioactivities of the different samples analyzed. This paper marks the first report on the chemical analysis of Helichrysum melaleucum species. Copyright © 2010 John Wiley & Sons, Ltd.
Investigation of surface topography differences in native and exotic invertebrates in the St. Lawrence River
Authors: Brown D. R. S. , Brown C. A.
Published: June 2010

The texture, or topography, interior of shells from native and exotic mollusks are measured and compared to determine if they can be discriminated. Area‐scale fractal analysis is used to calculate relative areas as a function of scale, and the relative areas are used to evaluate the measurements. Measurements from a scanning laser profiler and from confocal and interferometric microscopes are compared, as are measurements of an original and a replica. The relative areas indicate clear differences between the measurement instruments. The largest relative areas are calculated from the confocal measurements. The trueness of the measurements has not been determined. However, the relative areas calculated from the confocal measurements are capable of discriminating the native clam from the exotic mussels with a confidence of greater than 99% at scales below 10 µm2. SCANNING 32: 250–255, 2010. © 2010 Wiley Periodicals, Inc.
Fabrication and Mechanical Properties of Large‐Scale Freestanding Nanoparticle Membranes
Authors: He Jinbo , Kanjanaboos Pongsakorn , Frazer N. Laszlo , Weis Adam , Lin Xiao‐Min , Jaeger Heinrich M.
Published: June 2010

Thin‐film membranes consisting of nanoparticles are of interest in applications ranging from nanosieves to electric, magnetic, or photonic devices and sensors. However, the fabrication of large‐scale membranes in a simple but controlled way has remained a challenge, due to the limited understanding of their mechanical properties. Systematic experiments on ultrathin, freestanding nanoparticle membranes of different core materials, core sizes, and capping ligands are reported. The results demonstrate that a drying‐mediated self‐assembly process can be used to create close‐packed monolayer membranes that span holes tens of micrometers in diameter. Containing up to ≈107 particles, these freely suspended layers exhibit remarkable mechanical properties with Young's moduli of the order of several GPa, independent of membrane size. Comparison of three different core–ligand combinations suggests that the membrane's elastic response is set by how tightly the ligands are bound to the particle cores and by the ligand–ligand interactions.
Synovial Sarcoma Is a Stem Cell Malignancy
Authors: Naka Norifumi , Takenaka Satoshi , Araki Nobuhito , Miwa Toshitada , Hashimoto Nobuyuki , Yoshioka Kiyoko , Joyama Susumu , Hamada Ken-ichiro , Tsukamoto Yoshitane , Tomita Yasuhiko , Ueda Takafumi , Yoshikawa Hideki , Itoh Kazuyuki
Published: June 2010

Synovial sarcoma (SS) is a malignant soft tissue tumor characterized by its unique t(X;18)(p11;q11) chromosomal translocation leading to the formation of the SS18-SSX fusion gene. The resulting fusion protein product is considered to play as an aberrant transcription factor and transform target cells by perturbing their gene expression program. However, the cellular origin of SS is highly debated. We herein established two novel human SS cell lines, named Yamato-SS and Aska-SS, and investigated their biological properties. We found the self-renewal ability of these cells to generate sarcospheres, to form tumors in serial xenotransplantation and reconstitute the tumor phenotypes without fractionation by any surface markers. Both SS cells as well as clinical tissue specimens from 15 patients expressed the marker genes-associated stem cell identity, Oct3/4, Nanog, and Sox2. We also found that both SS cells displayed limited differentiation potentials for mesenchymal lineages into osteocytes and chondrocytes albeit with the expression of early mesenchymal and hematopoietic lineage genes. Upon SS18-SSX silencing with sequence-specific siRNAs, these SS cells exhibited morphological transition from spherical growth in suspension to adherent growth in monolayer, additional expression of later mesenchymal and hematopoietic lineage genes, and broader differentiation potentials into osteocytes, chondrocytes, adipocytes, and macrophages in appropriate differentiation cocktails. Collectively, these data suggest that a human multipotent mesenchymal stem cell can serve as a cell of origin for SS and SS is a stem cell malignancy resulting from dysregulation of self-renewal and differentiation capacities driven by SS18-SSX fusion protein.
Concise Review: Multiple Niches for Hematopoietic Stem Cell Regulations
Authors: Oh Il-Hoan , Kwon Kyung-Rim
Published: June 2010

Two types of stem cell niches in bone marrow (BM), endosteal osteoblastic, and vascular niches are involved in the microenvironmental regulation of hematopoietic stem cells (HSCs). Recently, redundant features of the two niches were identified, based on their common cellular origins or chemical mediators being produced in each niche. In contrast, studies have also revealed that HSCs are localized differentially in the niches with respect to their distinct functional status, and that the biological activity of each niche is differentially influenced by extrinsic conditions. An important question is, therefore, whether these two niches play distinct roles in regulating HSCs and whether they respond differentially to environmental stimuli/stress for “compartmentalized” niche organization in BM. In this review, recent discoveries related to the characteristics of each type of niche and their common or unique features are discussed, along with the possibility of multiniche regulation of HSCs in BM.