bluuebunny/crossref_metadata_2025_split huggingface dataset:
Familial summer-type hypersensitivity pneumonitis in Japan: two case reports and review of the literature
Authors: Nakajima Akira , Saraya Takeshi , Mori Takeshi , Ikeda Reiko , Sugita Takashi , Watanabe Takayasu , Fujiwara Masachika , Takizawa Hajime , Goto Hajime 
Published: September 2013

Abstract

Background
Hypersensitivity pneumonitis is defined as an allergic lung disease that occurs in response to inhalation of fungal antigens, bacterial antigens, chemicals, dusts, or animal proteins. The incidence of summer-type hypersensitivity pneumonitis is higher in the summer season, especially in Japan, due to the influence of the hot and humid environment and the common style of wood house or old concrete condominiums.

Case presentation
The present report describes a case of a middle-aged married couple who lived in the same house and who simultaneously suffered from summer-type hypersensitivity pneumonitis. This report analyzes these two cases in terms of environmental research and its microbiological, radiological, and pathological aspects. This case report is followed by a review of family occurrences of summer-type hypersensitivity pneumonitis from 22 studies with a total of 49 patients (including the two present cases) in Japan.

Conclusion
Summer-type hypersensitivity pneumonitis may be unrecognized and misdiagnosed as pneumonia or other respiratory diseases. A greater understanding of the clinical, pathologic, and environmental features of summer-type hypersensitivity pneumonitis might help improve diagnosis and delivery of appropriate management for this condition.
IDOMAL: the malaria ontology revisited
Authors: Topalis Pantelis , Mitraka Elvira , Dritsou Vicky , Dialynas Emmanuel , Louis Christos 
Published: September 2013

Abstract

Background
With about half a billion cases, of which nearly one million fatal ones, malaria constitutes one of the major infectious diseases worldwide. A recently revived effort to eliminate the disease also focuses on IT resources for its efficient control, which prominently includes the control of the mosquito vectors that transmit the Plasmodium pathogens. As part of this effort, IDOMAL has been developed and it is continually being updated.

Findings
In addition to the improvement of IDOMAL’s structure and the correction of some inaccuracies, there were some major subdomain additions such as a section on natural products and remedies, and the import, from other, higher order ontologies, of several terms, which were merged with IDOMAL terms. Effort was put on rendering IDOMAL fully compatible as an extension of IDO, the Infectious Disease Ontology. The reason for the difficulties in fully reaching that target were the inherent differences between vector-borne diseases and “classical” infectious diseases, which make it necessary to specifically adjust the ontology’s architecture in order to comprise vectors and their populations.

Conclusions
In addition to a higher coverage of domain-specific terms and optimizing its usage by databases and decision-support systems, the new version of IDOMAL described here allows for more cross-talk between it and other ontologies, and in particular IDO. The malaria ontology is available for downloading at the OBO Foundry (http://www.obofoundry.org/cgi-bin/detail.cgi?id=malaria_ontology) and the NCBO BioPortal (http://bioportal.bioontology.org/ontologies/1311).
In vitro parameter optimization for spatial control of focused ultrasound ablation when using low boiling point phase-change nanoemulsions
Authors: Puett Connor , Phillips Linsey C , Sheeran Paul S , Dayton Paul A 
Published: September 2013

Abstract

Background
Phase-shift nanoemulsions (PSNEs) provide cavitation sites when the perfluorocarbon (PFC) nanodroplets (ND) are vaporized to microbubbles by acoustic energy. Their presence lowers the power required to ablate tissue by high-intensity focused ultrasound (HIFU), potentially making it a safer option for a broader range of treatment sites. However, spatial control over the ablation region can be problematic when cavitation is used to enhance heating. This study explored relationships between vaporization, ablation, and the PSNE concentration in vitro to optimize the acoustic intensity and insonation time required for spatially controlled ablation enhancement using a PSNE that included a volatile PFC component.

Methods
HIFU (continuous wave at 1 MHz; insonation times of 5, 10, 15, and 20 s; cool-down times of 2, 4, and 6 s; peak negative pressures of 2, 3, and 4 MPa) was applied to albumin-acrylamide gels containing PFC agents (1:1 mix of volatile decafluorobutane and more stable dodecafluoropentane at 105 to 108 PFC ND per milliliter) or agent-free controls. Vaporization fields (microbubble clouds) were imaged by conventional ultrasound, and ablation lesions were measured directly by calipers. Controlled ablation was defined as the production of ‘cigar’-shaped lesions corresponding with the acoustic focal zone. This control was considered to be lost when ablation occurred in prefocal vaporization fields having a predominantly ‘tadpole’ or oblong shape.

Results
Changes in the vaporization field shape and location occurred on a continuum with increasing PSNE concentration and acoustic intensity. Working with the maximum concentration-intensity combinations resulting in controlled ablation demonstrated a dose-responsive relationship between insonation time and volumes of both the vaporization fields (approximately 20 to 240 mm3) and the ablation lesions (1 to 135 mm3) within them.

Conclusions
HIFU ablation was enhanced by this PSNE and could be achieved using intensities ≤650 W/cm2. Although the ablation lesions were located within much larger microbubble clouds, optimum insonation times and intensities could be selected to achieve an ablation lesion of desired size and location for a given PSNE concentration. This demonstration of controllable enhancement using a PSNE that contained a volatile PFC component is another step toward developing phase-shift nanotechnology as a potential clinical tool to improve HIFU.
Overexpression of a modified 6-phosphofructo-1-kinase results in an increased itaconic acid productivity in Aspergillus niger
Authors: van der Straat Laura , Tamayo-Ramos Juan A , Schonewille Tom , de Graaff Leo H 
Published: September 2013

Abstract
A modified 6-phosphofructo-1-kinase was expressed in a citrate producing Aspergillus niger strain in combination with cis-aconitate decarboxylase from Aspergillus terreus to study the effect on the production of itaconic acid. The modified pfkA gene was also expressed in combination with the itaconic acid biosynthetic cluster from A. terreus, which consists of cis- aconitate decarboxylase cadA, a putative mitochondrial transporter mttA and a putative plasmamembrane transporter mfsA. The combined expression of pfkA and cadA resulted in increased citrate levels, but did not show increased itaconic acid levels. The combined expression of pfkA with the itaconic acid biosynthetic cluster resulted in significantly increased itaconic acid production at earlier time points. Also the itaconic acid productivity increased significantly. The maximum itaconic acid productivity that was reached under these conditions was 0.15 g/L/h, which is only a factor 17 lower than the 2.5 g/L/h that according to the US Department of Energy should be achieved to have an economically feasible production process.
Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape
Authors: Day Kenneth , Waite Lindsay L , Thalacker-Mercer Anna , West Andrew , Bamman Marcas M , Brooks James D , Myers Richard M , Absher Devin 
Published: September 2013

Abstract
Background
DNA methylation is an epigenetic modification that changes with age in human tissues, although the mechanisms and specificity of this process are still poorly understood. We compared CpG methylation changes with age across 283 human blood, brain, kidney, and skeletal muscle samples using methylation arrays to identify tissue-specific age effects.

Results
We found age-associated CpGs (ageCGs) that are both tissue-specific and common across tissues. Tissue-specific ageCGs are frequently located outside CpG islands with decreased methylation, and common ageCGs show the opposite trend. AgeCGs are significantly associated with poorly expressed genes, but those with decreasing methylation are linked with higher tissue-specific expression levels compared with increasing methylation. Therefore, tissue-specific gene expression may protect against common age-dependent methylation. Distinguished from other tissues, skeletal muscle ageCGs are more associated with expression, enriched near genes related to myofiber contraction, and closer to muscle-specific CTCF binding sites. Kidney-specific ageCGs are more increasingly methylated compared to other tissues as measured by affiliation with kidney-specific expressed genes. Underlying chromatin features also mark common and tissue-specific age effects reflective of poised and active chromatin states, respectively. In contrast with decreasingly methylated ageCGs, increasingly methylated ageCGs are also generally further from CTCF binding sites and enriched within lamina associated domains.

Conclusions
Our data identified common and tissue-specific DNA methylation changes with age that are reflective of CpG landscape and suggests both common and unique alterations within human tissues. Our findings also indicate that a simple epigenetic drift model is insufficient to explain all age-related changes in DNA methylation.
Localization of CaSR Antagonists in CaSR-expressing Medullary Thyroid Cancer
Authors: Ding Haiming , Yusof Adlina Mohd , Kothandaraman Shankaran , Saji Motoyasu , Wang Chaojie , Kumar Krishan , Milum Keisha , Carleton Michelle , Pan Xueliang , Ringel Matthew D. , Tweedle Michael F. , Phay John E. 
Published: September 2013

Objective:
Image-based localization of medullary thyroid cancer (MTC) and parathyroid glands would improve the surgical outcomes of these diseases. MTC and parathyroid glands express high levels of calcium-sensing receptor (CaSR). The aim of this study was to prove the concept that CaSR antagonists specifically localize to CaSR-expressing tumors in vivo.

Design:
We synthesized two isomers of a known CaSR calcilytic, Calhex 231, and four new analogs, which have a favorable structure for labeling. Their antagonistic activity was determined using immunoblots demonstrating decreased ERK1/2 phosphorylation after calcium stimulation in human embryonic kidney cells overexpressing CaSR. Compound 9 was further radiolabeled with 125I and evaluated in nude mice with and without heterotransplanted xenografts of MTC cell lines, TT and MZ-CRC-1, that do and do not express CaSR, respectively.

Results:
Two newly synthesized compounds, 9 and 11, exhibited better antagonistic activity than Calhex 231. The half-life of 125I-compound 9 in nude mice without xenografts was 9.9 hours. A biodistribution study in nude mice bearing both tumors demonstrated that the uptake of radioactivity in TT tumors was higher than in MZ-CRC-1 tumors at 24 hours: 0.39 ± 0.24 vs 0.18 ± 0.12 percentage of injected dose per gram of tissue (%ID/g) (P = .002), with a ratio of 2.25 ± 0.62. Tumor-to-background ratios for TT tumors, but not MZ-CRC-1 tumors, increased with time. Tumor-to-blood values increased from 2.02 ± 0.52 at 1 hour to 3.29 ± 0.98 at 24 hour (P = .015) for TT tumors, and 1.7 ± 0.56 at 1 hour to 1.48 ± 0.33 at 24 hour (P = .36) for MZ-CRC-1 tumors.

Conclusions:
Our new CaSR antagonists specifically inhibit CaSR function in vitro, preferentially localize to CaSR-expressing tumors in vivo, and therefore have the potential to serve as scaffolds for further development as imaging pharmaceuticals.
Vitamin D3 Effects on Lipids Differ in Statin and Non-Statin-Treated Humans: Superiority of Free 25-OH D Levels in Detecting Relationships
Authors: Kane Lynn , Moore Kelly , Lütjohann Dieter , Bikle Daniel , Schwartz Janice B. 
Published: September 2013

Context:Inverse associations between 25-OH vitamin D levels and cardiovascular morbidity and mortality have been reported.Objectives:Our goals were to 1) investigate effects of correcting inadequate D status on lipids, 2) determine whether free 25-OH D is better correlated with lipids than total 25-OH D.Design:A randomized, double-blind placebo-controlled trial was performed.Setting:Participants resided in the general community.Participants:Adults with inadequate D status were randomized to D3: 14 men, 12 women, age 60 ± 8 years (mean ± SD) or placebo: 12 men, 11 women: 59 ±12 years.Intervention:Responses to 12-week oral vitamin D3 titrated (1000–3000 IU/d) to achieve 25-OH D levels ≥25 ng/mL were compared to placebo.Main Outcome Measures:Measurements were 25-OH D (tandem mass spectometry), free 25-OH D (direct immunoassay), lipids (directly measured triglyceride, cholesterol, and subfractions; plant sterols and cholesterol synthesis precursors), and safety labs before and after 6 and 12 weeks D3 or placebo. Data were analyzed by repeated measures ANOVA and linear regression.Results:Vitamin D3 was titrated to 1000 IU/d in 15/26 (58%), to 2000 IU/d in 10, and 3000 IU/d in one patient. D3 had no effect on cholesterol or cholesterol subfractions except for trends for decreases in atorvastatin-treated patients (cholesterol, P = .08; low-density lipoprotein [LDL] cholesterol, P = .05). Decreased campesterol concentrations (P = .05) were seen with D3 but not placebo in statin-treated patients. Relationships between total 25-OH D and lipids were not detected, but inverse linear relationships were detected between free 25-OH D and triglycerides (P = .03 for all participants [n = 49], P = .03 in all statin-treated [n = 19], and P = .0009 in atorvastatin-treated [n = 11]), and between free 25-OH D and LDL cholesterol (P = .08 overall, P = .02 in all statin-treated, and P = .03 for atorvastatin-treated), and total cholesterol (P = .09 overall; P = .04 for all statin-treated, and P = .05 for atorvastatin-treated).Conclusions:Vitamin D lipid-lowering effects appear limited to statin-treated patients and are likely due to decreased cholesterol absorption. Relationships between lipids and D metabolites were only detected when free 25-OH D was measured, suggesting the superiority of determining free 25-OH D levels compared to total 25-OH vitamin D levels when analyzing biologic responses.
Sinonasal Paraganglioma With Long-Delayed Recurrence and Metastases: Genetic and Imaging Findings
Authors: Michel Justin , Taïeb David , Jolibert Marianne , Torrents Julia , Wassef Michel , Morange Isabelle , Essamet Wassim , Barlier Anne , Dessi Patrick , Fakhry Nicolas 
Published: September 2013

Context:
Sinonasal paragangliomas have rarely been reported in the literature. They are often aggressive.

Patient:
We report an original case of sinonasal paragangliomas with a tumor recurrence diagnosed 13 years after resection of the primary tumor. Somatostatin receptor scintigraphy and [18F]-fluorodeoxyglucose positron emission tomography/computed tomography were the most sensitive functional imaging techniques, and they ruled out distant metastases. Interestingly, [18F]-fluorodihydroxyphenylalanine positron emission tomography/computed tomography was negative, a feature that may be considered a sign of functional dedifferentiation. Screening for germline mutations of the SDHB, SDHC, SDHD, SDHAF2, VHL, MAX, and TMEM127 was negative.

Conclusion:
The diagnosis of malignancy remains challenging at initial diagnosis, and patients should be followed during their entire lifetime.
Coordinated ventilation and spiracle activity produce unidirectional airflow in the hissing cockroach,Gromphadorhina portentosa
Authors: Heinrich Erica C. , McHenry Matthew J. , Bradley Timothy J. 
Published: September 2013

SummaryInsects exchange respiratory gases via an extensive network of tracheal vessels that open to the surface of the body through spiracular valves. Although gas exchange is known to increase with the opening of these spiracles, it is not clear how this event relates to gas flow through the tracheal system. We examined the relationship between respiratory airflow and spiracle activity in a ventilating insect, the hissing cockroach Gromphadorhina portentosa, to better understand the complexity of insect respiratory function. Using simultaneous video recordings of multiple spiracular valves, we found that abdominal spiracles open and close in unison during periods of ventilation. Additionally, independent recordings of CO2 release from the abdominal and thoracic regions, and observations of hyperoxic tracer gas movement, indicate that air is drawn into the thoracic spiracles and expelled from the abdominal spiracles. Our video recordings suggest that this unidirectional flow is driven by abdominal contractions that occur when the abdominal spiracles open. The spiracles then close as the abdomen relaxes and fills with air from the thorax. Therefore, the respiratory system of the hissing cockroach functions as a unidirectional pump through the coordinated action of the spiracles and abdominal musculature. This mechanism may be employed by a broad diversity of large insects that utilize active ventilation.
Spectral tuning of Amazon parrot feather coloration by psittacofulvin pigments and spongy structures
Authors: Tinbergen Jan , Wilts Bodo D. , Stavenga Doekele G. 
Published: September 2013

SummaryThe feathers of Amazon parrots are brightly coloured. They contain a unique class of pigments, the psittacofulvins, deposited in both barbs and barbules, causing yellow or red coloured feathers. In specific feather areas spongy nanostructured barb cells exist, reflecting either in the blue or blue-green wavelength range. The blue-green spongy structures are partly enveloped by a blue-absorbing, yellow-colouring pigment acting as a spectral filter, thus yielding a green coloured barb. Applying reflection and transmission spectroscopy, we characterized the Amazons' pigments and spongy structures, and investigated how they contribute to the feather coloration. The reflectance spectra of Amazon feathers are presumably tuned to the sensitivity spectra of the visual photoreceptors.
Exclusive localization of carbonic anhydrase in bacteriocytes of the deep-sea clamCalyptogena okutaniiwith thioautotrophic symbiotic bacteria
Authors: Hongo Yuki , Nakamura Yoshimitsu , Shimamura Shigeru , Takaki Yoshihiro , Uematsu Katsuyuki , Toyofuku Takashi , Hirayama Hisako , Takai Ken , Nakazawa Masatoshi , Maruyama Tadashi , Yoshida Takao 
Published: September 2013

SummaryDeep-sea Calyptogena clams harbor thioautotrophic intracellular symbiotic bacteria in their gill epithelial cells. The symbiont fixes CO2 to synthesize organic compounds. Carbonic anhydrase (CA) of the host catalyzes the reaction CO2 + H2O ↔ HCO3- + H+, and is assumed to facilitate inorganic carbon (Ci) uptake and transport to the symbiont. However, the localization of CA in gill tissue remains unknown. We therefore analyzed mRNA sequences, proteins and CA activity in Calyptogena okutanii using expression sequence tag, SDS-PAGE with LC-MS/MS. It was shown that acetazolamide-sensitive soluble CA was abundantly expressed in the gill tissue of C. okutanii, and the enzyme was purified by affinity chromatography. Mouse monoclonal antibodies against the CA of C. okutanii were used in Western blot analysis and immunofluorescence staining of the gill tissues of C. okutanii, showing that CA was exclusively localized in the symbiont-harboring cells (bacteriocytes) in gill epithelial cells. Western blot analysis and measurement of activity showed that CA was abundantly (26-72% of total soluble protein) detected in the gill tissues of not only Calyptogena clams but also deep-sea Bathymodiolus mussels that harbor thioautotrophic or methanotrophic symbiotic bacteria, but was not detected in a nonsymbiotic mussel, Mytilus sp. The present study showed that CA is abundant in the gill tissues of deep-sea symbiotic bivalves and specifically localizes in the cytoplasm of bacteriocytes of C. okutanii. These indicate that the Ci supply process to symbionts in the vacuole (symbiosome) in bacteriocytes is essential for symbiosis.
Effects of running on human Achilles tendon length-tension properties in the free and gastrocnemius components
Authors: Lichtwark Glen A. , Cresswell Andrew G. , Newsham-West Richard J. 
Published: September 2013

Summary
The elastic properties of the human Achilles tendon are important for locomotion, however in vitro tests suggest that repeated cyclic contractions lead to tendon fatigue; an increase in length in response to stress applied. In vivo experiments have not, however, demonstrated mechanical fatigue in the Achilles tendon, possibly due to the limitations of using two-dimensional ultrasound imaging to assess tendon strain. This study used freehand three-dimensional ultrasound (3DUS) to determine whether the free Achilles tendon (calcaneus to soleus) or the gastrocnemius tendon (calcaneus to gastrocnemius) demonstrated tendon fatigue after running exercise. Participants (n = 9) underwent 3DUS scans of the Achilles tendon during isometric contractions at four ankle torque levels (passive, 14, 42 and 70 N.m) before and after a 5 km run at a self selected pace (10-14km.h-1). Running had a significant main effect on the length of the free Achilles tendon (p &lt; 0.01) with a small increase in length across the torque range. However the mean lengthening effect was small (&lt;1%) and was not accompanied by a change in free tendon stiffness. There was no significant change in the length of the gastrocnemius tendon or the free tendon cross sectional area. While the free tendon was shown to lengthen, the lack of change in stiffness suggests the tendon exhibited mechanical creep rather than fatigue. These effects were much smaller than that predicted from in vitro experiments, possibly due to the different loading profile encountered and the ability of the tendon to repair in vivo.
NDE1 and NDEL1: twin neurodevelopmental proteins with similar ‘nature’ but different ‘nurture’
Authors: Bradshaw Nicholas J. , Hennah William , Soares Dinesh C. 
Published: September 2013

AbstractNuclear distribution element 1 (NDE1, also known as NudE) and NDE-like 1 (NDEL1, also known as Nudel) are paralogous proteins essential for mitosis and neurodevelopment that have been implicated in psychiatric and neurodevelopmental disorders. The two proteins possess high sequence similarity and have been shown to physically interact with one another. Numerous lines of experimental evidence in vivo and in cell culture have demonstrated that these proteins share common functions, although instances of differing functions between the two have recently emerged. We review the key aspects of NDE1 and NDEL1 in terms of recent advances in structure elucidation and cellular function, with an emphasis on their differing mechanisms of post-translational modification. Based on a review of the literature and bioinformatics assessment, we advance the concept that the twin proteins NDE1 and NDEL1, while sharing a similar ‘nature’ in terms of their structure and basic functions, appear to be different in their ‘nurture’, the manner in which they are regulated both in terms of expression and of post-translational modification within the cell. These differences are likely to be of significant importance in understanding the specific roles of NDE1 and NDEL1 in neurodevelopment and disease.