Miracle-dz/UniFAR-FTUs huggingface dataset:
Conformational Cycle of the Vitamin B12 ABC Importer in Liposomes Detected by Double Electron-Electron Resonance (DEER)*

Background: Type II ABC importers transport diverse substrates into the cell. Results: EPR on BtuCD-F in liposomes shows the response of cytoplasmic gate II during nucleotide cycle in the presence of substrate. Conclusion: The cytoplasmic gate II closes with substrate and ATP as in the x-ray structure. Substrate can be released after hydrolysis. Significance: There is new insight into the mechanism of transport in membranes. Double electron-electron resonance is used here to investigate intermediates of the transport cycle of the Escherichia coli vitamin B12 ATP-binding cassette importer BtuCD-F. Previously, we showed the ATP-induced opening of the cytoplasmic gate I in TM5 helices, later confirmed by the AMP-PNP-bound BtuCD-F crystal structure. Here, other key residues are analyzed in TM10 helices (positions 307 and 322) and in the cytoplasmic gate II, i.e. the loop between TM2 and TM3 (positions 82 and 85). Without BtuF, binding of ATP induces detectable changes at positions 307 and 85 in BtuCD in liposomes. Together with BtuF, ATP triggers the closure of the cytoplasmic gate II in liposomes (reported by both positions 82 and 85). This forms a sealed cavity in the translocation channel in agreement with the AMP-PNP·BtuCD-F x-ray structure. When vitamin B12 and AMP-PNP are simultaneously present, the extent of complex formation is reduced, but the short 82–82 interspin distance detected indicates that the substrate does not affect the closed conformation of this gate. The existence of the BtuCD-F complex under these conditions is verified with spectroscopically orthogonal nitroxide and Gd(III)-based labels. The cytoplasmic gate II remains closed also in the vanadate-trapped state, but it reopens in the ADP-bound state of the complex. Therefore, we suggest that the substrate likely trapped in ATP·BtuCD-F can be released after ATP hydrolysis but before the occluded ADP-bound conformation is reached.
Profiles of Connectedness: Processes of Resilience and Growth in Children With Cancer.

OBJECTIVE Identified patterns of connectedness in youth with cancer and demographically similar healthy peers. METHOD Participants included 153 youth with a history of cancer and 101 youth without a history of serious illness (8-19 years). Children completed measures of connectedness, posttraumatic stress symptoms (PTSS), and benefit-finding. Parents also reported on children's PTSS. RESULTS Latent profile analysis revealed four profiles: high connectedness (45%), low connectedness (6%), connectedness primarily to parents (40%), and connectedness primarily to peers (9%). These profiles did not differ by history of cancer. However, profiles differed on PTSS and benefit-finding. Children highly connected across domains displayed the lowest PTSS and highest benefit-finding, while those with the lowest connectedness had the highest PTSS, with moderate PTSS and benefit-finding for the parent and peer profiles. CONCLUSION Children with cancer demonstrate patterns of connectedness similar to their healthy peers. Findings support connectedness as a possible mechanism facilitating resilience and growth.
The impact of khat use on East African communities in Melbourne: a preliminary investigation.

INTRODUCTION AND AIMS Catha Edulis Forsk (khat) is a plant-reported to have a stimulant effect similar to that of amphetamines-grown and used by eastern African communities worldwide. Khat can be legally consumed in many parts of the world, including Victoria, Australia. Recent concerns have been raised about the social and economic impacts of khat consumption among Victoria's East African community members. This study explores khat use and the social impact it has on East African families and communities in Melbourne, Australia. DESIGN AND METHODS Focus groups and individual interviews were conducted in 2009 with 29 members of Melbourne's East African community recruited via community leaders and snowball sampling. Fifty-five per cent of the sample reported khat use and the remainder reported only having experience of other people's use of the drug. RESULTS Participants who did not report chewing khat were mainly concerned with the negative social impacts of its use, such as the extended time men spent away from their families while consuming the drug. These participants (mainly women) expressed their hope that khat would be prohibited in Victoria. Participants who reported the use of khat (mainly men) reported that any social problems existed independently of khat consumption. DISCUSSION AND CONCLUSIONS This study found only limited evidence that khat use has been impacting directly on people's health and well-being. Any moves to prohibit khat use may further marginalise already vulnerable groups of people.
Electrohydrodynamic Injection Micropump With Composite Gold and Single-Walled Carbon Nanotube Electrodes

The presence of microfeatures/nanofeatures with sharp asperities on the emitter electrodes of ion drag electrohydrodynamic (EHD) micropumps is likely to enhance the local electric field and charge injection significantly, and thus the pressure generation and flow rates. The objective of this paper is to investigate the performance of EHD micropumps with single-walled carbon nanotubes (SWCNT) on the emitter electrodes. The micropumps had 100 pairs of planar electrodes where the width of the emitter and collector electrodes was 20 and 40 μm, respectively, with a cross-sectional domain of 100 μm × 5 mm. Two micropumps with interelectrode spacing of 120 and 40 μm were tested with a smooth emitter surface, and where SWCNT were electrophoretically deposited on the emitter electrodes using HFE7100 as the working fluid. The threshold voltage for charge injection lowered by a factor of 3 and 1.4 for the two pumps with SWCNT on the emitter electrodes compared with the smooth electrode case. The corresponding static pressure head increased by a factor 5, while the flow rate at no external back pressure increased by a factor 3 for the pump with interelectrode spacing of 120 μm. For the pump with interelectrode spacing of 40 μm, a maximum static pressure of 4.7 kPa was achieved at 900 V with SWCNT on the emitter electrode.
Lifetime recreational exercise activity and risk of breast carcinoma in situ

The incidence rates of breast carcinoma in situ (BCIS) have increased dramatically over the past two decades, primarily because of increased mammography screening. Ductal carcinoma in situ, which accounts for approximately 85% of BCIS and 10–20% of all breast carcinomas, is generally recognized as the final step in the progression to invasive disease. To the authors' knowledge, few studies have been conducted to date to evaluate BCIS risk factors. Because of its potential effects on circulating sex hormones, physical activity has been proposed as a modifiable risk factor for invasive breast carcinoma. However, the relation to BCIS risk is poorly understood.
Primary Cutaneous Peripheral T-Cell Lymphoma With Aberrant Coexpression of CD20: Case Report and Review of the Literature

We report an unusual case of primary cutaneous T-cell lymphoma in a 45-year-old male showing expression of the B-cell marker CD20. The lesion presented as a large plaque on the right shin and rapidly developed into additional lesions on the right lower leg and right anterior chest. Despite therapy, bone involvement was discovered at 1 year after initial presentation. Punch biopsy of the right leg revealed a diffuse, atypical dermal lymphocytic infiltrate with papillary edema and no epidermotropism. The atypical cells strongly expressed the T-cell markers CD3, CD2, and CD43, with additional expression of cytotoxic T-cell markers CD8, cytotoxic granule-associated RNA binding protein (TIA-1), and granzyme B and loss of CD7 by immunohistochemistry (IHC). In addition, the atypical cells with the above phenotype exhibited moderate expression of CD20 by IHC. Coexpression of CD8 and CD20 in the atypical cells was confirmed by a dual-labeled IHC stain. Clonal rearrangements of the T-cell receptor γ- and β-chain genes were detected by polymerase chain reaction; however, there was no expression of T-cell receptor β-chain identified by IHC. In conclusion, we present a case a of CD8-positive primary cutaneous T-cell lymphoma with CD20 expression, exhibiting aggressive behavior.
High-dose methotrexate in adult oncology patients: A case-control study assessing the risk association between drug interactions and methotrexate toxicity

Introduction High-dose methotrexate, defined as dose ≥1 g/m2, is commonly used in chemotherapy protocols. Certain drugs such as acyclovir, allopurinol, proton pump inhibitors and some antibiotics have been associated with delayed renal clearance of methotrexate and may predispose patients to toxicities. Currently, no specific recommendations exist on adjusting the high-dose methotrexate regimen in the presence of potential interacting drugs. This study aims to determine whether presence of interacting drugs is associated with delayed methotrexate clearance. Methods This was a case-control study of adult oncology patients who received their first cycle of high-dose methotrexate. Cases were defined as patients who experienced delayed methotrexate clearance, as indicated by serum methotrexate level ≥ 0.1 umol/L at 72 h. The primary endpoint was the frequency of presence of interacting drugs between cases and controls. These were compared using Fisher's exact test. Where possible, adjustment for significant baseline differences that can affect methotrexate clearance was made using logistic regression. The secondary endpoint was frequency of methotrexate-related clinical toxicities between groups and included myelosuppression, nephrotoxicity, hepatotoxicity and mucositis. Results From January 2004 to March 2011, 73 patients met study criteria, of which 23 were defined as cases. Significant baseline differences were methotrexate dose received (9116 mg ± 4339 versus 6054 mg ± 2874, p=0.012) and renal impairment (5 versus 0, p = 0.002). The presence of interacting drugs was not associated with delayed methotrexate clearance (OR 0.91, 95% CI 0.24–3.38, p > 0.999). After adjusting for methotrexate dose, drugs observed more frequently (allopurinol, proton pump inhibitors and sulfamethoxazole/trimethoprim) were not associated with delayed methotrexate clearance (p = 0.95, 0.59 and 0.20, respectively). Cases experienced more severe anemia (grade 2.52 versus 1.68, p = 0.007) and higher rates of mucositis (65.2% versus 20.0%, p < 0.001). Conclusion This study showed no significant association between presence of interacting drugs and delayed methotrexate clearance. Patients who experienced delayed methotrexate clearance had higher incidence of severe anemia and mucositis.
Fossil forests in the Austral Basin (Argentina) marking a Cenomanian heterogeneous forced regressive surface

The mid‐Cretaceous greenhouse period in the southern Patagonia Argentina (Austral Basin) is represented by the Mata Amarilla Formation. It is composed of three informal sections which were deposited in littoral and continental environments. The boundary between the lower and middle sections of the Mata Amarilla Formation shows a drastic reduction in accommodation/sediment supply (A/S) ratio, interpreted as a forced regressive surface. This surface is characterized by a well‐developed palaeosol, associated with the extensive preservation of a podocarp‐dominated fossil forest over a vast area (more than 5400 km2). Sedimentological and palaeopedological analyses, in conjunction with forest structure, tree density and growth ring analyses, indicate that the mid‐Cenomanian forced regression can be distinguished as a non‐uniform surface developed over a short period of time. This sequence boundary is recognized through a heterogeneous regional surface, delimited in the western part of the study area by an erosional surface generated by a large lateral channel migration recorded by sheet‐like channel deposits with transported logs. By comparison, towards the eastern part of the study area, it appears as a paraconformity bounded by a very mature vertic Alfisol, which may have taken 40–100 ky to develop, and the preservation of a fossil forest in life position with a minimum age of 337 years. It is concluded that the extensive presence of these fossil forests at the same stratigraphic level in a vast region respond to changes in A/S ratio in a forced regressive surface at basin scale.
Partial- and full-mouth scaling and root planing in type 2 diabetic subjects: a 12-mo follow-up of clinical parameters and levels of cytokines and osteoclastogenesis-related factors.

BACKGROUND AND OBJECTIVE The aim of this study was to evaluate the effects of full-mouth scaling and root planing (FMSRP) and partial-mouth scaling and root planing (PMSRP), up to 12 mo after treatment, on clinical parameters, and levels of cytokines and osteoclastogenesis-related factors in type 2 diabetic subjects with chronic periodontitis. MATERIAL AND METHODS Thirty-four subjects received FMSRP (n = 17) or PMSRP (n = 17) within 24 h or in multiple sessions, respectively. Clinical parameters and local levels of tumor necrosis factor-α (TNF-α), interferon-γ (IFN-γ), interleukin (IL)-17, IL-23, IL-4, receptor activator of NF-β ligand and osteoprotegerin were assessed at baseline, and 3, 6 and 12 mo after therapies. RESULTS Clinical parameters improved after both therapies (p < 0.05), and no between-group differences were observed at any time-point (p > 0.05). Overall, there were no considerable differences in the local levels of the biomarkers studied between groups (p > 0.05). The IL-23 concentration and total amount of IFN-γ increased in the FMSRP group and decreased in the PMSRP group from baseline to 3 mo and from baseline to 6 mo, respectively (p < 0.05). CONCLUSION Both PMSRP and FMSRP promoted benefits in clinical parameters and showed a similar modulation of cytokines and osteoclastogenesis-related factors at 12 mo in type 2 diabetic subjects.
Abecarnil, a metabolically stable, anxioselective beta-carboline acting at benzodiazepine receptors.

Abecarnil (isopropyl 6-benzyloxy-4-methoxymethyl-beta-carboline-3-carboxylate) is a novel ligand for central benzodiazepine (BZ) receptors, possessing anxiolytic and anticonvulsant properties, but with considerably reduced muscle relaxant effects in comparison to diazepam (DZP). In vitro, abecarnil inhibited the binding of the BZ [3H]lormetazepam to rat cerebral cortex membranes with an IC50 value of 0.82 nM in comparison to 56 nM for DZP. The ability of abecarnil to displace [3H]lormetazepam was enhanced 1.24-fold in the presence of 30 microM gamma-aminobutyric acid; the corresponding value for DZP was 2.8-fold. DZP and abecarnil were equally effective in enhancing the binding of t-[35S]butylbicyclophosphorothionate to rat cortical membranes. In vivo, abecarnil exhibited a 3- to 6-fold higher affinity to forebrain BZ receptors than DZP. Abecarnil was from 2 to 10 times more potent than DZP in most rodent tests of anxiolytic activity, and in reducing locomotor activity in mice and rats thoroughly habituated to the test chamber. However, in rats newly exposed to a novel cage, abecarnil was less potent than DZP in reducing locomotor activity. In tests of motor coordination, abecarnil, in contrast to DZP, showed no or only weak activity, and in potentiating the effects of ethanol and hexobarbital on motor performance abecarnil was 4 to 25 times less potent than DZP. Abecarnil antagonized the effects of BZs in the chimney and loss of righting reflex tests, but not in the rotarod test. (ABSTRACT TRUNCATED AT 250 WORDS)
Effectiveness of dementia follow-up care by memory clinics or general practitioners: randomised controlled trial

Objective To examine the effectiveness of post-diagnosis dementia treatment and coordination of care by memory clinics compared with general practitioners. Design Multicentre randomised controlled trial. Setting Nine memory clinics and 159 general practitioners in the Netherlands. Participants 175 patients with a new diagnosis of mild to moderate dementia living in the community and their informal caregivers. Interventions Usual care provided by memory clinic or general practitioner. Main outcome measures Caregiver rated quality of life of the patient measured with the quality of life in Alzheimer’s disease instrument and self perceived burden of the informal caregiver measured with the sense of competence questionnaire (intention to treat analysis). Results The quality of life of the patients in the memory clinic group was 0.5 (95% confidence interval −0.7 to 1.6) points higher than in the general practitioner group. Caregivers’ burden was 2.4 (−5.8 to 1.0) points lower in the memory clinic group than in the general practitioner group. Conclusion No evidence was found that memory clinics were more effective than general practitioners with regard to post-diagnosis treatment and coordination care for patients with dementia. Without further evidence on the effectiveness of these modalities, other arguments, such as cost minimisation, patients’ preferences, or regional health service planning, can determine which type of dementia care is offered. Trial registration Clinical trials NCT00554047.
X‐ray crystallographic validation of structure predictions used in computational design for protein stabilization

Protein engineering aimed at enhancing enzyme stability is increasingly supported by computational methods for calculation of mutant folding energies and for the design of disulfide bonds. To examine the accuracy of mutant structure predictions underlying these computational methods, crystal structures of thermostable limonene epoxide hydrolase variants obtained by computational library design were determined. Four different predicted effects indeed contributed to the obtained stabilization: (i) enhanced interactions between a flexible loop close to the N‐terminus and the rest of the protein; (ii) improved interactions at the dimer interface; (iii) removal of unsatisfied hydrogen bonding groups; and (iv) introduction of additional positively charged groups at the surface. The structures of an eightfold and an elevenfold mutant showed that most mutations introduced the intended stabilizing interactions, and side‐chain conformations were correctly predicted for 72–88% of the point mutations. However, mutations that introduced a disulfide bond in a flexible region had a larger influence on the backbone conformation than predicted. The enzyme active sites were unaltered, in agreement with the observed preservation of catalytic activities. The structures also revealed how a c‐Myc tag, which was introduced for facile detection and purification, can reduce access to the active site and thereby lower the catalytic activity. Finally, sequence analysis showed that comprehensive mutant energy calculations discovered stabilizing mutations that are not proposed by the consensus or B‐FIT methods. Proteins 2015; 83:940–951. © 2015 Wiley Periodicals, Inc.
Respiratory morbidity in rubber workers: II. Pulmonary function in curing workers.

Pulmonary function tests were conducted on 121 curing and 189 control workers in 1972; 87% of the 1972 cohort was resurveyed one year later. The curing workers were subdivided into high and low exposure groups on the basis of environmental sampling. Cross-sectionally, in the 1972 cohort, the residual forced vital capacity was significantly decreased (P greater than .01) among the the heavily exposed workers (266 ml). Longitudinally, the mean one-year loss of forced expiratory volume in one second (FEV1.0) (173 ml/yr) in the curing workers with more than ten years of exposure was significantly greater (P less than .01) than in the control groups. Pulmonary function tests before and after a day's work were conducted on 29 curing-room workers. The eight heavily exposed curing workers had a significant decrease (P less than .05) in FEV1.0 of 115 ml. Our findings are sufficient to conclude that heavy exposure to curing fume affects pulmonary function. We recommend reduction of exposure and further longitudinal studies, especially in regard to those most heavily exposed.
Second-Site Mutagenesis of a Hypomorphic argonaute1 Allele Identifies SUPERKILLER3 as an Endogenous Suppressor of Transgene Posttranscriptional Gene Silencing1[OPEN]

Addressing RNAs to the 3′-to-5′ exoribonuclease of the cytoplasmic exosome counteracts posttranscriptional transgene silencing. Second-site mutagenesis was performed on the argonaute1-33 (ago1-33) hypomorphic mutant, which exhibits reduced sense transgene posttranscriptional gene silencing (S-PTGS). Mutations in FIERY1, a positive regulator of the cytoplasmic 5′-to-3′ EXORIBONUCLEASE4 (XRN4), and in SUPERKILLER3 (SKI3), a member of the SKI complex that threads RNAs directly to the 3′-to-5′ exoribonuclease of the cytoplasmic exosome, compensated AGO1 partial deficiency and restored S-PTGS with 100% efficiency. Moreover, xrn4 and ski3 single mutations provoked the entry of nonsilenced transgenes into S-PTGS and enhanced S-PTGS on partially silenced transgenes, indicating that cytoplasmic 5′-to-3′ and 3′-to-5′ RNA degradation generally counteract S-PTGS, likely by reducing the amount of transgene aberrant RNAs that are used by the S-PTGS pathway to build up small interfering RNAs that guide transgene RNA cleavage by AGO1. Constructs generating improperly terminated transgene messenger RNAs (mRNAs) were not more sensitive to ski3 or xrn4 than regular constructs, suggesting that improperly terminated transgene mRNAs not only are degraded from both the 3′ end but also from the 5′ end, likely after decapping. The facts that impairment of either 5′-to-3′ or 3′-to-5′ RNA degradation is sufficient to provoke the entry of transgene RNA into the S-PTGS pathway, whereas simultaneous impairment of both pathways is necessary to provoke the entry of endogenous mRNA into the S-PTGS pathway, suggest poor RNA quality upon the transcription of transgenes integrated at random genomic locations.
Contribution of galactoglycerolipids to the 3‐dimensional architecture of thylakoids

Thylakoid membranes, the universal structure where photosynthesis takes place in all oxygenic photosynthetic organisms from cyanobacteria to higher plants, have a unique lipid composition. They contain a high fraction of 2 uncharged glycolipids, the galactoglycerolipids mono‐ and digalactosyldiacylglycerol (MGDG and DGDG, respectively), and an anionic sulfolipid, sulfoquinovosediacylglycerol (SQDG). A remarkable feature of the evolution from cyanobacteria to higher plants is the conservation of MGDG, DGDG, SQDG, and phosphatidylglycerol (PG), the major phospholipid of thylakoids. Using neutron diffraction on reconstituted thylakoid lipid extracts, we observed that the thylakoid lipid mixture self‐organizes as a regular stack of bilayers. This natural lipid mixture was shown to switch from hexagonal II toward lamellar phase on hydration. This transition and the observed phase coexistence are modulated by the fine‐tuning of the lipid profile, in particular the MGDG/DGDG ratio, and by the hydration. Our analysis highlights the critical role of DGDG as a contributing component to the membrane stacking via hydrogen bonds between polar heads of adjacent bilayers. DGDG interactions balance the repulsive electrostatic contribution of the charged lipids PG and SQDG and allow the persistence of regularly stacked membranes at high hydration. In developmental contexts or in response to environmental variations, these properties can contribute to the highly dynamic flexibility of plastid structure. —Demé, B. , Cataye, C. , Block, M. A. , Maréchal, E. , Jouhet, J. Contribution of galactoglycerolipids to the 3‐dimensional architecture of thylakoids. FASEB J. 28, 3373–3383 (2014). www.fasebj. org