Miracle-dz/UniFAR-FTUs huggingface dataset:
Variable temperature effects of Open Top Chambers at polar and alpine sites explained by irradiance and snow depth

Environmental manipulation studies are integral to determining biological consequences of climate warming. Open Top Chambers (OTCs) have been widely used to assess summer warming effects on terrestrial biota, with their effects during other seasons normally being given less attention even though chambers are often deployed year‐round. In addition, their effects on temperature extremes and freeze‐thaw events are poorly documented. To provide robust documentation of the microclimatic influences of OTCs throughout the year, we analysed temperature data from 20 studies distributed across polar and alpine regions. The effects of OTCs on mean temperature showed a large range (−0.9 to 2.1 °C) throughout the year, but did not differ significantly between studies. Increases in mean monthly and diurnal temperature were strongly related (R2 = 0.70) with irradiance, indicating that PAR can be used to predict the mean warming effect of OTCs. Deeper snow trapped in OTCs also induced higher temperatures at soil/vegetation level. OTC‐induced changes in the frequency of freeze‐thaw events included an increase in autumn and decreases in spring and summer. Frequency of high‐temperature events in OTCs increased in spring, summer and autumn compared with non‐manipulated control plots. Frequency of low‐temperature events was reduced by deeper snow accumulation and higher mean temperatures. The strong interactions identified between aspects of ambient environmental conditions and effects of OTCs suggest that a detailed knowledge of snow depth, temperature and irradiance levels enables us to predict how OTCs will modify the microclimate at a particular site and season. Such predictive power allows a better mechanistic understanding of observed biotic response to experimental warming studies and for more informed design of future experiments. However, a need remains to quantify OTC effects on water availability and wind speed (affecting, for example, drying rates and water stress) in combination with microclimate measurements at organism level.
Effect of Solution Chemistry on the Extent of Binding of Phenanthrene by a Soil Humic Acid: A Comparison of Dissolved and Clay Bound Humic

The effect of pH, ionic strength, and cation in solution on the binding of phenanthrene by a soil humic acid in the aqueous phase was determined using fluorescence quenching. The phenanthrene binding coefficient with the dissolved soil humic, Koc, decreased with increasing ionic strength and solution cation valence. At low values of ionic strength, Koc values for this soil humic acid increased with increasing pH. For this humic sample, the experimental results were consistent with a conformational model of the humic substance in aqueous solution where, depending on solution conditions, some parts of the humic structure may be more open to allow increased PAH access to attachment sites. After sorption onto clays, supernatant solutions of the unadsorbed humic fraction yielded lower Koc values than the original bulk humic acid, suggesting that the humic substance was fractionating during its sorption onto the clays. Additionally, the extent of phenanthrene binding with the adsorbed humic fraction was lower t.
Molecular imaging of pulmonary nodules.

OBJECTIVE Lung nodules can be benign or malignant, reflecting many possible causes, ranging from inflammatory and infectious processes to neoplasms. Incidental detection on chest x-ray or thoracic CT often requires further evaluation by imaging or invasive procedures. CONCLUSION Currently, 18F-FDG PET/CT offers both anatomic and metabolic characterization of lung nodules. Fluorine-18-thymidine, 11C-methionine, 68Ga-DOTA-somatostatin analogs, and 18F-dihydroxyphenylalanine may offer additional molecular information useful for diagnosis and treatment planning.
Specificity of retroviral RNA packaging

Encapsidation of retroviral RNA has been shown to be dependent on specific cis-acting signals, in particular, the packaging region (psi) located near the 5' end of the retroviral genome. In this report, we show that a 683-base avian extended packaging sequence (psi+) derived from Rous sarcoma virus will direct packaging of heterologous hygromycin mRNA into avian virions when present at the 3' end of the transcript in the sense orientation. However, this packaging is not as efficient as the packaging of RNA encoded by a standard avian retroviral vector. A quail cell line containing a Rous sarcoma virus mutant, SE21Q1b, produces virions which will package endogenous cellular mRNAs randomly, roughly in proportion to their intracellular concentrations. We found that viral particles from SE21Q1b retain the capacity to specifically encapsidate hygromycin mRNAs containing the avian psi+. To determine whether packaging of cellular mRNA would occur in other retroviral packaging lines, we assayed virion RNA isolated from the retroviral particles produced by avian and murine packaging lines for the presence of endogenous cellular mRNAs. Endogenous cellular mRNAs were not found randomly packaged into virions produced by any of the packaging lines examined except SE21Q1b. Some specific sequences, however, were found packaged into avian virions. Endogenous retrovirus-related mink cell focus-inducing murine leukemia virus RNAs and 30S viruslike RNAs were found to be efficiently packaged into murine virions even in the presence of RNAs containing all cis-acting retroviral sequences.
The Effect of Spectral Quality on Daily Patterns of Gas Exchange, Biomass Gain, and Water-Use-Efficiency in Tomatoes and Lisianthus: An Assessment of Whole Plant Measurements

Advancements in light-emitting diode (LED) technology have made them a viable alternative to current lighting systems for both sole and supplemental lighting requirements. Understanding how wavelength specific LED lighting can affect plants is thus an area of great interest. Much research is available on the wavelength specific responses of leaves from multiple crops when exposed to long-term wavelength specific lighting. However, leaf measurements do not always extrapolate linearly to the complexities which are found within a whole plant canopy, namely mutual shading and leaves of different ages. Taken together, both tomato (Solanum lycopersicum) leaves under short-term illumination and lisianthus (Eustoma grandiflorum) and tomato whole plant diurnal patterns of plants acclimated to specific lighting indicate wavelength specific responses of both H2O and CO2 gas exchanges involved in the major growth parameters of a plant. Tomato leaves grown under a white light source indicated an increase in transpiration rate and internal CO2 concentration and a subsequent decrease in water-use-efficiency (WUE) when exposed to a blue LED light source compared to a green LED light source. Interestingly, the maximum photosynthetic rate was observed to be similar. Using plants grown under wavelength specific supplemental lighting in a greenhouse, a decrease in whole plant WUE was seen in both crops under both red-blue (RB) and red-white (RW) LEDs when compared to a high pressure sodium (HPS) light. Whole plant WUE was decreased by 31% under the RB LED treatment for both crops compared to the HPS treatment. Tomato whole plant WUE was decreased by 25% and lisianthus whole plant WUE was decreased by 15% when compared to the HPS treatment when grown under RW LED. The understanding of the effects of wavelength specific lighting on both leaf and whole plant gas exchange has significant implications on basic academic research as well as commercial greenhouse production.
Comorbidity between neurological illness and psychiatric disorders

Psychiatric disorders are common in many neurological disorders, including epilepsy, migraine, Alzheimer’s disease, Parkinson’s disease, essential tremor, and stroke. These comorbidities increase disease burden and may complicate the treatment of the combined disorders. Initial studies of the comorbidity of psychiatric and neurological disorders were cross-sectional, and time order of the associations was impossible to elucidate. More recent work has clarified time associations between psychiatric disorders and neurological disorders, particularly in epilepsy and stroke where epidemiological evidence suggests that there is a bidirectional relationship. This article takes an epidemiological approach to understanding these relationships and focuses mostly on epilepsy. Although, these relationships are understood in many neurological disorders, routine screening for psychiatric disorders in neurological disorders is infrequent, mostly due to the lack of partnerships between psychiatrists and neurologists and the paucity of neuropsychiatrists. Much more needs to be done to improve the detection and treatment of patients affected by neurological and psychiatric disorders. Understanding the scope of this overlap may inspire collaborations to improve the lives of people affected by both disorders.
Analysis of D1853N ATM polymorphism in radiosensitive patients with cervical carcinoma.

UNLABELLED Clinical oncologists have been focusing their efforts on attempting to define risk groups of patients with unusual biological reactions to the recommended therapy regimens using molecular biology techniques. THE AIMS OF OUR STUDY WERE (i) to find a design and validate a method for fast and reliable analysis of the D1853N (5557G>A) genetic polymorphism in the ATM (ataxia-telangiectasia mutated) gene; (ii) to use side-directed mutagenesis to generate ATM 5557A-positive DNA (reference ATM5557A DNA); and (iii) to analyze a group of patients suffering from cervical carcinoma with adverse responses to radiotherapy. The 5557A variant was found in three of twenty women (15%). Our data show that the prevalence of the 5557A allelic variant in cervical cancer subjects with adverse responses after irradiation probably does not differ from the prevalence common in Caucasians. A larger population study should confirm these preliminary results.
Instructional Practices in Mainstreamed Secondary Classrooms

This study examined the skills of secondary students that teachers considered necessary for success in mainstreamed regular education classrooms and intervention strategies teachers would be willing to use. Teachers (N=89) from three high schools rated the importance of 14 student skills and the reasonability of 35 intervention strategies. Student skills deemed important included following directions, coming to class prepared with materials, using class time wisely, and making up assignments and tests. Factor analysis of intervention strategy results revealed seven factors: using supplemental resources; simplifying instruction; providing support and extra instructional cues; enhancing classroom behavior management; facilitating grade improvement; modifying learning environment; and teaching study skills and providing a positive, cooperative learning environment. Secondary teachers appear to prefer intervention strategies that they can implement in their own classroom, that can apply to all students, and that require little extra time.
Studies on phenylketonuria. I. Restricted phenylalanine intake in phenylketonuria.

The relationship between the biochemical defect in the.hereditary condition, phenylketonuria (phenylpyruvic oligophrenia), and the accompanying mental defect is at the present time obscure. The work of F6lling (1) and Jervis (2, 3) has shown that the inheritance of the condition appears to be controlled by a single autosomal recessive gene. A series of investigations by Jervis and his collaborators (4-1 ) has demonstrated that the biochemical defect lies in a failure of the affected individuals to oxidize phenylalanine to tyrosine in the normal fashion. The major abnormal metabolites known to occur in this condition can arise as a logical consequence of the accumulation of large amounts of phenylalanine and the channelling of this phenylalanine into abnormal pathways. These metabolites are phenylalanine itself (8), phenylpyruvic acid (8), phenyllactic acid (8), and phenylacetylglutamine (12). Abnormally high levels of phenylalanine are found in serum (20 to 60 mg. per 100 ml.) and cerebrospinal fluid (6 to 8 mg. per 100 ml.) (9) and phenylpyruvic acid has been demonstrated in the serum of affected individuals (10). Recently it has been found that lesser amounts of other abnormal metabolites are excreted. These include o-hydroxyphenylacetic acid (13, 14) and products derived from tyrosine (13, 15) and tryptophan (15, 16). The manner in which these substances arise will be considered in later communications.
Structure–activity relationships for abiotic thiol reactivity and aquatic toxicity of halo-substituted carbonyl compounds

Using abiotic thiol reactivity (EC50) and Tetrahymena pyriformis toxicity (IGC50) data for a group of halo-substituted ketones, esters and amides (i.e. SN2 electrophiles) and related compounds a series of structure–activity relationships are illustrated. Only the α-halo-carbonyl-containing compounds are observed to be thiol reactive with the order I > Br > Cl > F. Further comparisons disclose α-halo-carbonyl compounds to be more reactive than non-α-halo-carbonyl compounds; in addition, the reactivity is reduced when the number of C atoms between the carbonyl and halogen is greater than one. Comparing reactivity among α-halo-carbonyl-containing compounds with different β-alkyl groups shows the greater the size of the β-alkyl group the lesser the reactivity. A comparison of reactivity data for 2-bromoacetyl-containing compounds of differing dimensions reveals little difference in reactivity. Regression analysis demonstrates a linear relationship between toxicity and thiol reactivity: ; n = 19, s = 0.250, r 2 = 0.926, r 2(pred) = 0.905, F = 199, Pr > F = 0.0001. ‖Presented at the 12th International Workshop on Quantitative Structure--Activity Relationships in Environmental Toxicology (QSAR2006), 8--12 May 2006, Lyon, France.
Prevalence and behavioural risk factors of Staphylococcus aureus nasal colonization in community-based injection drug users

SUMMARY The aims of this study were to identify Staphylococcus aureus nasal colonization prevalence, behavioural risk factors, and to determine staphylococcal protein A (spa) types in community-based injection drug users (IDUs). Nasal swabs were collected and methicillin susceptibility testing and spa/SCCmec typing were performed on S. aureus isolates. Generalized estimating equations were used to report adjusted odds ratios and 95% confidence intervals. Of the 440 participants, 24·1% were colonized and 5·7% had methicillin-resistant S. aureus (MRSA). Colonization was associated with age, employment/marital status, and the presence of scabs but not with sexually transmitted disease co-infection, HIV status, antibiotic use, hospitalization, or drug treatment programme participation. The USA300 MRSA clone spa types were most common, but 15/49 spa types were new to one of the international databases. Community-based IDUs appear to have different risk factors compared to IDUs from clinical studies. In addition, the number of newly identified spa types indicates a diverse, understudied population.
H1,K1-ATPase (Proton Pump) Is the Target Autoantigen of Th1-Type Cytotoxic T Cells in Autoimmune Gastritis

MARIO M. D’ELIOS,* MATHIJS P. BERGMAN, ‡ ANNALISA AZZURRI,* AMEDEO AMEDEI,* MARISA BENAGIANO,* JAN J. DE PONT,§ FABIO CIANCHI, \ CHRISTINA M. VANDENBROUCKE–GRAULS, ‡ SERGIO ROMAGNANI,* BEN J. APPELMELK,‡ and GIANFRANCO DEL PRETE* Departments of *Internal Medicine and \Surgery, University of Florence, Florence, Italy; ‡Department of Medical Microbiology, Vrije Universiteit, Medical School, Amsterdam, The Netherlands; and §Department of Biochemistry, University of Nijmegen, Nijmegen, The Netherlands
Restless legs syndrome and daytime sleepiness are prominent in myotonic dystrophy type 2

Lam et al.1 studied the frequency of restless legs syndrome, excessive daytime sleepiness (EDS), and fatigue in 30 patients with myotonic dystrophy type 2 (DM2). They did not find obstructive sleep apnea (OSA) or REM sleep behavior disorder. The authors concluded that EDS may also be related to an intrinsic CNS disturbance in DM2. We found that OSA is the most frequent sleep-disordered breathing (SDB) in this disorder. By home-based cardiorespiratory monitoring, we found SDB in 6 …
Bearing fault prognostics based on signal complexity and Gaussian process models

Standard bearing fault detection features are shown to be ineffective for estimating bearings remaining useful life (RUL). Addressing this issue, in this paper we propose an approach for bearing fault prognostics based on features describing the statistical complexity of the envelope of the generated vibrations and a set of Gaussian process (GP) models. The proposed feature set exhibits continuous trend which can be directly related to the deterioration of bearing condition. Gaussian process models are non-parametric black-box models which differ from most other frequently used black-box identification approaches as they search for the relationships among measured data rather than trying to approximate the modeled system by fitting the parameters of the selected basis functions. Their output is normal distribution, expressed in terms of mean and variance, which can be interpreted as a confidence in prediction. In this paper the GP models are used for filtering noisy features and estimating the RUL based on filtered features. The proposed approach was evaluated on the data set provided for the IEEE PHM 2012 Prognostic Challenge.
Update in clinical allergy and immunology

In the recent years, a tremendous body of studies has addressed a broad variety of distinct topics in clinical allergy and immunology. In this update, we discuss selected recent data that provide clinically and pathogenetically relevant insights or identify potential novel targets and strategies for therapy. The role of the microbiome in shaping allergic immune responses and molecular, as well as cellular mechanisms of disease, is discussed separately and in the context of atopic dermatitis, as an allergic model disease. Besides summarizing novel evidence, this update highlights current areas of uncertainties and debates that, as we hope, shall stimulate scientific discussions and research activities in the field.
A phase II study of high dose tamoxifen and weekly cisplatin in patients with metastatic melanoma

We have previously demonstrated that the combination of tamoxifen and cisplatin has activity in patients with metastatic melanoma. In vitro studies have demonstrated that tamoxifen and cisplatin exhibit cytotoxic synergy in human melanoma cells and that this interaction is dependent on a tamoxifen effect. The mechanism of this effect is currently under investigation in in vitro studies. In an attempt to improve the complete response rate of this regimen, we initiated a phase II trial to determine the effect of the use of high dose tamoxifen and weekly cisplatin on the complete response rate, disease-free survival and overall survival. Tamoxifen was started on day 1 initially at a dose of 240 mg/day and continued until the patient was taken off treatment. This dose was subsequently lowered to 200 mg/day. Cisplatin (80 mg/m2) was begun on day 2 and repeated weekly for a total of 3 weeks. During week 4, the patient was not treated with cisplatin but was evaluated for response. If disease stabilization or regression was documented, the patient received a second 3 week cycle of cisplatin and was then re-evaluated for response. Patients with progressive disease at any evaluation were removed from the study. In 28 consecutive patients, the overall response rate was 32% (95% confidence interval 15.88–52.35%). One patient achieved a complete remission that lasted 22 months. All other responses were partial in nature. Toxicity was primarily nausea and vomiting. Two patients developed grade 2 renal toxicity. There were no episodes of deep venous thrombosis. This phase II study demonstrates that this combination has modest activity in patients with metastatic melanoma. However, this study failed to confirm our hypothesis that high dose tamoxifen would increase the complete response rate of this combination. While this combination has activity, the overall response rate is not significantly better that that observed with the original Dartmouth regimen and the toxicity is substantial. We do not recommend this dose and schedule for routine clinical use.
Immunologic Changes Occurring at Kindergarten Entry Predict Respiratory Illnesses after the Loma Prieta Earthquake

Previous studies in adult populations have demonstrated alterations in immune function after psychologically stressful events, and pediatric research has shown significant associations between stress and various childhood morbidities. However, no previous work has examined stress-related immune changes in children and subsequent illness experience. Twenty children were enrolled in a study on immunologic changes after kindergarten entry and their prospective relationship to respiratory illness (Rl) experience. Midway through a 12-week Rl data collection period, the October 17, 1989 Loma Prieta earthquake occurred. The timing of this event created a natural experiment enabling us to study possible associations between immunologic changes at kindergarten entry, the intensity of earthquake-related stress for children and parents, and changes in Rl incidence over the 6 weeks after the earthquake. Immunologic changes were measured using helper (CD4+)-suppressor (CD8+) cell ratios, lymphocyte responses to pokeweed mitogen, and type-specific antibody responses to Pneumovax, in blood sampled 1 week before and 1 week after school entry. Rl incidence was assessed using home health diaries and telephone interviews completed every 2 weeks. Rls per child varied from none to six. Six children showed an increase in Rl incidence after the earthquake; five experienced a decline. Changes in helper-suppressor cell ratios and pokeweed mitogen response predicted changes in Rl incidence in the postearthquake period (r = .43, .46; p < .05). Children showing upregulation of immune parameters at school entry sustained a significant increase in Rl incidence after the earthquake. These findings suggest that individual differences in immune reactivity to a minor normative stressor may be related to the rate of infection after a major stressful event. J Dev Behav Pediatr 14:296–303, 1993. Index terms: stress, respiratory infection, psychoneuroimmunology.