nils-herrmann/clean_scirepeval huggingface dataset:
The structure of a redundant enzyme: a second isoform of aspartate beta-semialdehyde dehydrogenase in Vibrio cholerae.

Aspartate-beta-semialdehyde dehydrogenase (ASADH) is an essential enzyme that is found in bacteria, fungi and plants but not in humans. ASADH produces the first branch-point metabolite in the biosynthetic pathways that lead to the production of lysine, threonine, methionine and isoleucine as well as the cell-wall precursor diaminopimelate. As a consequence, ASADH appears to be an excellent target for the development of novel antibiotics, especially for Gram-negative bacteria that require diaminopimelate for cell-wall biosynthesis. In contrast to the Gram-negative ASADHs, which readily formed well diffracting crystals, the second isoform of aspartate-beta-semialdehyde dehydrogenase from Vibrio cholerae (vcASADH2) was less well behaved in initial crystallization trials. In order to obtain good-quality single crystals of vcASADH2, a buffer-optimization protocol was used in which the initial purification buffer was exchanged into a new condition derived from a pre-crystalline hit. The unliganded structure of vcASADH2 has been determined to 2.2 A resolution to provide additional insight into the structural and functional evolution of the ASADH enzyme family. The overall fold and domain organization of this new structure is similar to the Gram-negative, Gram-positive and archeal ASADH structures determined previously, despite having less than 50% sequence identity to any of these family members. The substrate-complex structure reveals that the binding of L-aspartate-beta-semialdehyde (ASA) to vcASADH2 is accommodated by structural changes in the amino-acid binding site and in the helical subdomain that is involved in the dimer interface. Structural alignments show that this second isoform from Gram-negative V. cholerae most closely resembles the ASADH from a Gram-positive organism and is likely to bind the coenzyme in a different conformation to that observed in the other V. cholerae isoform.

Field of study: Chemistry
Herschel observations of EXtra-Ordinary Sources: Analysis of the HIFI 1.2 THz Wide Spectral Survey Toward Orion KL II. Chemical Implications

We present chemical implications arising from spectral models fit to the Herschel/HIFI spectral survey toward the Orion Kleinmann-Low nebula (Orion KL). We focus our discussion on the eight complex organics detected within the HIFI survey utilizing a novel technique to identify those molecules emitting in the hottest gas. In particular, we find the complex nitrogen bearing species CH_3CN, C_2H_3CN, C_2H_5CN, and NH_2CHO systematically trace hotter gas than the oxygen bearing organics CH_3OH, C_2H_5OH, CH_3OCH_3, and CH_3OCHO, which do not contain nitrogen. If these complex species form predominantly on grain surfaces, this may indicate N-bearing organics are more difficult to remove from grain surfaces than O-bearing species. Another possibility is that hot (T_(kin) ~ 300 K) gas phase chemistry naturally produces higher complex cyanide abundances while suppressing the formation of O-bearing complex organics. We compare our derived rotation temperatures and molecular abundances to chemical models, which include gas-phase and grain surface pathways. Abundances for a majority of the detected complex organics can be reproduced over timescales ≳10^5 years, with several species being underpredicted by less than 3σ. Derived rotation temperatures for most organics, furthermore, agree reasonably well with the predicted temperatures at peak abundance. We also find that sulfur bearing molecules that also contain oxygen (i.e., SO, SO_2, and OCS) tend to probe the hottest gas toward Orion KL, indicating the formation pathways for these species are most efficient at high temperatures.

Field of study: Physics
Thermorecovery of cyanobacterial fatty acids at elevated temperatures.

We have developed a genetic system we call "thermorecovery" that allows us to lyse cyanobacterial cultures and hydrolyze membrane lipids to release free fatty acids (FFAs), a biofuel precursor. The system uses thermostable lipases encoded by genes from thermophilic organisms that have been transferred into the cyanobacterial genome and can be synthesized by turning off CO(2) availability and subsequently activated by increasing the concentrated culture temperature. When synthesized in FFA-producing strains, the lipase Fnl from Fervidobacterium nodosum Rt17-B1 released the most FFA. Of the seven candidate lipases investigated, Fnl-synthesizing strains yielded 42.7±1.5 mg/l FFA at 47°C. We also determined that the optimal production conditions for SD338, the Synechocystis strain synthesizing Fnl, was to keep the cell concentrates at 46°C for two days after a one-day CO(2) limitation pretreatment of the culture. A 4-l continuous semi-batch production experiment with SD338 showed that daily harvested cultures (1l) released an average of 43.9±6.6 mg fatty acid and this productivity lasted for at least 20 days without significant decline. This improved thermorecovery process can be used in conjunction with other means to genetically engineer cyanobacteria to produce biofuels or biofuel precursors as the final step in recovery of membrane lipids.

Field of study: Biology, Engineering
Mother's Milk: An Existential Perspective on Negative Reactions to Breast-Feeding

Drawing from an existential perspective rooted in terror management theory, four studies examined the hypothesis that breast-feeding women serve as reminders of the physical, animal nature of humanity and that such recognition is threatening in the face of one's unalterable mortality. Study 1 demonstrated that mortality salience (MS) led to more negative reactions toward a scenario depicting a woman breast-feeding her infant in public, and in Study 2, MS decreased liking and increased physical avoidance of a potential task partner described as breast-feeding in another room. Further supporting the hypothesis that such reactions are rooted in threats associated with human creatureliness, MS in conjunction with a breast-feeding prime led to an increase in the accessibility of creaturely related cognitions (Study 3) and priming human/animal similarities (i.e., creatureliness) led to increased negativity toward a magazine cover depicting a woman breast-feeding her child (Study 4). Implications of this research are discussed.

Field of study: Psychology
Improving Federalism: Drivers of Change, Repair Options and Reform Scenarios

The Academy of Social Sciences in Australia (ASSA) and the Institute of Public Administration Australia (IPAA) hosted a ‘Policy Roundtable on Federalism’ on the 17–18 May 2007 at the University of Canberra. Around 50 attended the roundtable comprising politicians, Commonwealth and state public servants, and academics. The roundtable was provided with a number of background papers including the Hollander-Patapan article and another produced by staff of the Commonwealth Grants Commission entitled ‘Trends in Commonwealth-State Financial Relations: a Grants Commission Perspective’. The roundtable focused not only on issues and challenges but, more practically, on options and how to make federalism work better.

Field of study: Political science
Improved regularized solution of the inverse problem in turbidimetric measurements.

We present results of simulation research on the constrained regularized least-squares (RLS) solution of the ill-conditioned inverse problem in turbidimetric measurements. The problem is formulated in terms of the discretized Fredholm integral equation of the first kind. The inverse problem in turbidimetric measurements consists in determining particle size distribution (PSD) function of particulate system on the basis of turbidimetric measurements. The desired PSD should satisfy two constraints: nonnegativity of PSD values and normalization of PSD to unity when integrated over the whole range of particle size. Incorporating the constraints into the RLS method leads to the constrained regularized least-squares (CRLS) method, which is realized by means of an active set algorithm of quadratic programming. Results of simulation research prove that the CRLS method performs considerably better with reconstruction of PSD than the RLS method in terms of better fidelity and smaller uncertainty.

Field of study: Physics
African Monsoon Multidisciplinary Analysis: An International Research Project and Field Campaign

African Monsoon Multidisciplinary Analysis (AMMA) is an international project to improve our knowledge and understanding of the West African monsoon (WAM) and its variability with an emphasis on daily-to-interannual time scales. AMMA is motivated by an interest in fundamental scientific issues and by the societal need for improved prediction of the WAM and its impacts on West African nations. Recognizing the societal need to develop strategies that reduce the socioeconomic impacts of the variability of the WAM, AMMA will facilitate the multidisciplinary research required to provide improved predictions of the WAM and its impacts. This will be achieved and coordinated through the following five international working groups: i) West African monsoon and global climate, ii) water cycle, iii) surface–atmosphere feedbacks, iv) prediction of climate impacts, and v) high-impact weather prediction and predictability. AMMA promotes the international coordination of ongoing activities, basic research, and a...

Field of study: Environmental science
Human impact on tropical-alpine plant diversity in the northern Andes

Conserving páramo diversity and ecosystem services in the northern Andes is urgent, and understanding factors that control vegetation changes is therefore crucial. Although anthropogenic activities have been common in the Andean highlands for centuries, the role of human influence in shaping páramo vegetation remains unclear. To assess the relative importance of human disturbance associated with cattle farming and cultivation for plant species diversity and composition, we analyzed variables driven by both natural and human impact in the Santurbán páramo, Colombia. Canonical correspondence analysis (CCA) showed that the main gradient in plant species composition is related to the gradient of human impact. Partial CCA showed that the pure effect of the variables driven by human impact on floristic composition is twice the size of the pure effect of the variables driven by natural impact. Forward selection procedure indicated that the impact of human disturbance on floristic composition is determined by the level of accessibility. Vegetation patterns are driven by a complex set of elevation-related environmental factors, and human disturbance plays a primary role. Strict protection should be granted to remote and upper sites of the páramo. Restriction of fire and agriculture along steep slopes may counteract negative effects of human disturbance on plant species diversity.

Field of study: Environmental science
Identification and Visualization of the Underlying Independent Causes of the Diagnostic of Diabetic Retinopathy made by a Deep Learning Classifier

Interpretability is a key factor in the design of automatic classifiers for medical diagnosis. Deep learning models have been proven to be a very effective classification algorithm when trained in a supervised way with enough data. The main concern is the difficulty of inferring rationale interpretations from them. Different attempts have been done in last years in order to convert deep learning classifiers from high confidence statistical black box machines into self-explanatory models. In this paper we go forward into the generation of explanations by identifying the independent causes that use a deep learning model for classifying an image into a certain class. We use a combination of Independent Component Analysis with a Score Visualization technique. In this paper we study the medical problem of classifying an eye fundus image into 5 levels of Diabetic Retinopathy. We conclude that only 3 independent components are enough for the differentiation and correct classification between the 5 disease standard classes. We propose a method for visualizing them and detecting lesions from the generated visual maps.

Field of study: Computer science
Explicit feedback and the management of uncertainty in meeting climate objectives with solar geoengineering

Solar geoengineering has been proposed as a method of meeting climate objectives, such as reduced globally averaged surface temperatures. However, because of incomplete understanding of the effects of geoengineering on the climate system, its implementation would be in the presence of substantial uncertainties. In our study, we use two fully coupled atmosphere–ocean general circulation models: one in which the geoengineering strategy is designed, and one in which geoengineering is implemented (a real-world proxy). We show that regularly adjusting the amount of solar geoengineering in response to departures of the observed global mean climate state from the predetermined objective (sequential decision making; an explicit feedback approach) can manage uncertainties and result in achievement of the climate objective in both the design model and the real-world proxy. This approach results in substantially less error in meeting global climate objectives than using a predetermined time series of how much geoengineering to use, especially if the estimated sensitivity to geoengineering is inaccurate.

Field of study: Environmental science
Nitric oxide inhalation inhibits inducible nitric oxide synthase but not nitrotyrosine formation and cell apoptosis in rat lungs with meconium-induced injury

To investigate the effects of inhaled nitric oxide (NO) on pulmonary inflammation, apoptosis, peroxidation and protein nitration in a rat model of acute lung injury (ALI) induced by meconium.Twenty-four healthy male Sprague-Dawley rats were randomly devided into 3 groups (n=8): meconium-induced ALI with intratracheal instillation of 1 mL/kg saline (Mec/saline group), continuous inhalation of NO at 20 μL/L. (Mec/iNO), and the control group (control). Electromicroscopic examination was used to determine the extent of epithelial apoptosis. TUNEL was used to detect DNA fragmentation in pulmonary apoptotic cells, expressed as the apoptosis index (AI). Western blotting was used to detect pulmonary inducible NO synthase (iNOS) expression. RT-PCR was used to detect interleukin (IL)-1β mRNA expression. Cell count inbronchoalveolar lavage (BAL), myeloperoxidase (MPO) activity, as well as malondialdehyde (MDA) and nitrotyrosine formation, the markers of toxic NO-superoxide pathway in rat lung parenchyma specimens, were also examined.Expression of iNOS protein and IL-1β mRNA were increased significantly in the Mec/saline group (both P<0.01) compared with the control group. BAL cell count, MPO activity, lung injury score, pulmonary AI, MDA level and nitrotyrosine formation were also increased significantly (all P<0.01). The meconium-induced iNOS protein and IL-1β mRNA expression were inhibited significantly by NO inhalation when compared with the Mec/saline group (both P<0.01). BAL cell count, MPO activity and lung injury score were also decreased significantly (P<0.01 or P<0.05). However, there were no statistical differences in MDA level, nitrotyrosine formation or pulmonary AI between the Mec/saline and Mec/iNO groups. Electromicroscopic examination revealed a significant degree of epithelial apoptosis in both the Mec/saline and Mec/iNO groups.Early continuous inhalation of NO 20 μL/L may protect the lungs from inflammatory injury, but does not decrease epithelial apoptosis or lung nitrotyrosine formation. Inhalation of NO alone is not associated with a detectable increase in oxidant stress.

Field of study: Biology, Chemistry, Medicine
Alcohol consumption is enhanced after naltrexone treatment.

It is well known that alcohol increases opioid activity, which can contribute to the reinforcing effect of alcohol. Clinical studies have supported reductions in alcohol consumption among alcoholic patients during treatment with opioid antagonists (OAs) and its use is recommended for this purpose. Experimental studies have demonstrated opioid receptor up-regulation after several days of OA treatment, which increases the availability of these receptors. On this basis, the physiological conditions in the period immediately after the OA treatment could increase the reinforcing value of alcohol and in this way enhance alcohol consumption.



To test this hypothesis, 2 groups of Wistar male rats were used in the present study. After assessing the baseline of voluntary alcohol (10% v/v) consumption, subjects were treated with either the OA naltrexone (Ntx), (2 mg/kg/d/rat) or a saline solution (0.2 mL/d/male) for 7 days. Subsequently, all subjects were given a free choice between ethanol (10%) and water for 5 days. To study a possible cumulative effect, this procedure was sequentially repeated 4 times with each group. Water and food were available ad libitum throughout the experiment.



After each period of 7 days of Ntx use, alcohol consumption increased significantly with respect to the baseline and each equivalent period in the control group. When the subjects were exposed to alcohol again 1 week after the last of the 4 sequential periods, alcohol drinking was higher than the baseline in the Ntx group, but not in the control group. Water consumption was decreased during Ntx treatment in the control group in periods 1, 2, and 4. Food intake and body weight did not show differences between groups throughout the study; however, a decrease in food intake was observed over time regardless of treatment.



These results show that alcohol intake may increase after the Ntx treatment, particularly when alcohol is not available during treatment with the OA, and that this may be due to a higher availability of opioid receptors in that period.

Field of study: Medicine
BIAS IN LINEAR MODEL POWER AND SAMPLE SIZE CALCULATION DUE TO ESTIMATING NONCENTRALITY.

Data analysts frequently calculate power and sample size for a planned study using mean and variance estimates from an initial trial. Hence power, or the sample size needed to achieve a fixed power, varies randomly. Such calculations can be very inaccurate in the General Linear Univariate Model (GLUM). Biased noncentrality estimators and censored power calculations create inaccuracy. Censoring occurs if only certain outcomes of an initial trial lead to a power calculation. For example, a confirmatory study may be planned (and a sample size estimated) only following a significant result in the initial trial. Computing accurate point estimates or confidence bounds of GLUM noncentrality, power, or sample size in the presence of censoring involves truncated noncentral F distributions. We recommend confidence bounds, whether or not censoring occurs. A power analysis of data from humans exposed to carbon monoxide demonstrates the substantial impact on sample size that may occur. The results highlight potential biases and should aid study planning and interpretation.

Field of study: Mathematics
Regioselective Synthesis of Dimethylamino‐ or Arylalkylamino‐‘‘Crowned” Tröger's Base Analogues Under Vilsmeier–Haack Conditions

Under typical Vilsmeier–Haack conditions, Troger's base undergoes regioselective dimethylamino or arylalkylamino substitution on the methano bridge of the dibenzo[b,f][1,5]diazocine system, revealing a hitherto unknown reactivity pattern. The regioselectivity of the reaction was established by NMR spectroscopy and X-ray crystallography. The key feature of this reaction is its generality; it is compatible with different substitution patterns on the Troger's base and can be performed with DMF as well as with other formamides. The wide scope of the reaction has been applied in the synthesis of several uncommon Troger's base analogues.

Field of study: Chemistry
Development of Sensitive Monoclonal Antibody-based Enzyme-linked Immunosorbent Assay for Renal Toxicity Ingredient Aristolochic acid A in Chinese Herb Medicine

Aristolochic acid A-bovine serum albumin (BSA) conjugate and aristolochic acid A-ovalbumin (OVA) conjugate,were produced as the immunogen and coating antigen,respectively. A monoclonal antibody (mAb),designated as 1A11,was produced with aristolochic acid A-BSA. The titer was 2×104. The mAb was IgG1 isotype with κ light chains. A sensitive monoclonal antibody-based indirected enzyme-linked immunosorbent assay (icELISA) was established with the mAb. The cross-reactivity (CR) of mAb 1A11 with aristolochic acid B,C and D,an analog of aristolochic acid A,was 2.8%,3.5% and 31.2%,respectively. IC50 and the working range of the icELISA for aristolochic acid A were 1.9 and 0.5-7.5 μg/L,respectively. The average recoveries of aristolochic acid A fortified in caulis clematidis armandii were 86%-97% with RSD of 5.2%-11.1%. Analysis of aristolochic acid A in Chinese herb medicines and Chinese proprietary medicines with icELISA showed that the examined samples of manshurian dutchmanspipe stem,herba aristolochiae,fructus aristolochiae,aristolochia fangchi,and dutchmanspipe root were positive,the caulis clematidis armandii and the other Chinese proprietary medicines examined samples were negative and the results were confirmed by HPLC analysis. This ELISA is suitable for the rapid detection of aristolochic acid A in Chinese Herb medicine.

Field of study: Chemistry
Gonadal steroids regulate GABAA receptor subunit mRNA expression in NT2-N neurons.

Changes in gonadal steroid hormone levels during the menstrual cycle affect seizure frequency in women with catamenial epilepsy. Since GABA(A) receptors (GABARs) contribute to the prevention and termination of seizures by reducing neuronal excitability, we hypothesized that fluctuating gonadal steroid levels might affect GABAR subunit expression, which could alter inhibitory tone leading to increased seizure activity. To address this question in a simplified environment in vitro, we examined the effects of gonadal steroids on NT2-N neuronal cells. We have previously shown that NT2-N cells express functional GABARs, and that the expression pattern of GABAR subunits is regulated by chronic benzodiazepine exposure and hypoxia. NT2-N neurons were exposed to progesterone (0.1 microM), beta-estradiol (3 nM), or vehicle (DMSO) for 2 days or 7 days prior to RNA harvesting. GABAR subunit mRNA levels were assessed by semiquantitative RT-PCR normalized to actin levels. Progesterone exposure for 7 days increased alpha2 and gamma3 and decreased alpha5 subunit mRNAs, while beta-estradiol caused significant increases in alpha3, beta3 and epsilon expression. Further analysis revealed differential regulation of alpha4, alpha5, epsilon and pi subunit expression. Plots of relative PCR density in progesterone-treated cells for alpha2 vs. alpha5, alpha5 vs. gamma3 and alpha2 vs. gamma3 showed correlation between samples, suggesting coordinate regulation. Both progesterone and estrogen nuclear receptor mRNAs were detected by RT-PCR, and 2 days but not 7 days estrogen exposure upregulated progesterone receptor mRNA. Gonadal steroid fluctuations regulate GABA(A) receptor subunit expression in NT2-N cells. Such changes, if observed in vivo, could affect seizure frequency.

Field of study: Biology
Low-Loss Multilayer Dielectric Mirrors

The preparation of low-loss multilayer dielectric coatings for laser mirrors is described. Layer thickness is controlled by a unique monitoring system utilizing a 6328-A gas laser as a light source. Experiments designed to evaluate and reduce losses in the mirror coatings are discussed. It is found that mirror transmission losses may be reduced to a negligible value by deposition of a sufficient number of dielectric layers, without at the same time increasing scattering and absorption losses. Reflectivities in excess of 99.8% have been obtained from a single stack of twenty-five quarter-wave layers. Broad-band mirrors with reflectivities greater than 99.5% from 4300 A to 7400 A have been produced by properly stacking two such twenty-five-layer groups.

Field of study: Physics