Miracle-dz/UniFAR-FTUs huggingface dataset:
A β-Alanine Catabolism Pathway Containing a Highly Promiscuous ω-Transaminase in the 12-Aminododecanate-Degrading Pseudomonas sp. Strain AAC

ABSTRACT We previously isolated the transaminase KES23458 from Pseudomonas sp. strain AAC as a promising biocatalyst for the production of 12-aminododecanoic acid, a constituent building block of nylon-12. Here, we report the subsequent characterization of this transaminase. It exhibits activity with a broad substrate range which includes α-, β-, and ω-amino acids, as well as α,ω-diamines and a number of other industrially relevant compounds. It is therefore a prospective candidate for the biosynthesis of a range of polyamide monomers. The crystal structure of KES23458 revealed that the protein forms a dimer containing a large active site pocket and unusual phosphorylated histidine residues. To infer the physiological role of the transaminase, we expressed, purified, and characterized a dehydrogenase from the same operon, KES23460. Unlike the transaminase, the dehydrogenase was shown to be quite selective, catalyzing the oxidation of malonic acid semialdehyde, formed from β-alanine transamination via KES23458. In keeping with previous reports, the dehydrogenase was shown to catalyze both a coenzyme A (CoA)-dependent reaction to form acetyl-CoA and a significantly slower CoA-independent reaction to form acetate. These findings support the original functional assignment of KES23458 as a β-alanine transaminase. However, a seemingly well-adapted active site and promiscuity toward unnatural compounds, such as 12-aminododecanoic acid, suggest that this enzyme could perform multiple functions for Pseudomonas sp. strain AAC. IMPORTANCE We describe the characterization of an industrially relevant transaminase able to metabolize 12-aminododecanoic acid, a constituent building block of the widely used polymer nylon-12, and we report the biochemical and structural characterization of the transaminase protein. A physiological role for this highly promiscuous enzyme is proposed based on the characterization of a related gene from the host organism. Molecular dynamics simulations were carried out to compare the conformational changes in the transaminase protein to better understand the determinants of specificity in the protein. This study makes a substantial contribution that is of interest to the broad biotechnology and enzymology communities, providing insights into the catalytic activity of an industrially relevant biocatalyst as well as the biological function of this operon.
Hepatic arterial administration of sorafenib and iodized oil effectively attenuates tumor growth and intrahepatic metastasis in rabbit VX2 hepatocellular carcinoma model.

AIM To investigate the therapeutic effect of the hepatic arterial administration of sorafenib in rabbit VX-2 hepatocellular carcinoma (HCC) model. METHODS Rabbit VX-2 HCC models were established via implanting VX-2 tumors into the livers, and randomly divided into four groups, respectively treated with (1) The hepatic arterial administration of iodized oil alone (TACE-i), (2) The hepatic arterial administration of iodized oil and pharmorubicin (TACE-ip), (3) The hepatic arterial administration of iodized and cis-DDP (TACE-ic), (4) The hepatic arterial administration of iodized and sorafenib (TACE-is). The growth rate and intrahepatic metastasis of implanted VX-2 tumor in each rabbit were measured. Microvessel density (MVD) in the adjacent tissues of implanted VX-2 tumor were estimated by detecting the expression of CD34 and VEGF level in tumor adjacent tissues were also examined by Immunohistochemistry. RESULTS Compared with other groups, TACE-is treatment group presented a better effect on inhibiting tumor growth rate and intrahepatic metastasis in rabbit VX-2 HCC model. The angiogenesis (assessed by MVD) in the adjacent tissues were suppressed more dramatically in TACE-is treated group. Moreover, TACE-is treatment did not significantly increase the levels of alanine transaminase and creatinine compared to the group with TACE-i treatment. CONCLUSION The hepatic arterial administration of sorafenib and iodized oil (TACE-is) effectively attenuates tumor growth and intrahepatic metastasis in rabbit VX-2 HCC model without obvious hepatic and renal toxicity. One of the related mechanisms may be due to the inhibition of angiogenesis in the adjacent tissues. Our data indicated that TACE-is may be a secure and effective treatment for HCC.
Prevalence and Determinants of Elevated Gamma-Glutamyl Transferase in Chinese Hypertensive Adults

Objectives: This study aims to examine the prevalence and determinants of elevated gamma-glutamyl transferase (GGT) in 11,901 Chinese hypertensive adults aged 45-75 years. Methods: A cross-sectional investigation was carried out in the rural area of Lianyungang, China. Elevated GGT was defined as a GGT level ≥50 IU/L. Results: The prevalence of elevated GGT was 11.2% (4.9% in women and 21.9% in men). Median GGT level was 23.0 IU/L (20.0 IU/L in women and 29.0 IU/L in men). In multivariable logistic-regression models, abdominal obesity (waist circumference ≥90 cm), obesity (body mass index ≥25 kg/m 2 ), current drinking, residents inland (vs. coastal), and greater red meat consumption were important independent risk factors for elevated GGT in both genders. For other risk factors, gender-related differences were observed. Older age in men was inversely associated with elevated GGT, and women with antihypertensive treatment had a higher prevalence of elevated GGT. Physical activity levels were negatively correlated to GGT levels in men and women. In addition, there was a positive interaction effect between current smoking and current drinking (P=0.037) or waist circumference (≥90 cm vs.<90 cm, P<0.001) in GGT levels between men and women. Conclusions: In conclusion, there was a high prevalence of elevated GGT in Chinese hypertensive adults, particularly in participants from inland (vs. coastal) areas. A detrimentally interactive effect between current smoking and current drinking or abdominal obesity in GGT levels was also observed.
FaCoY – A Code-to-Code Search Engine

Code search is an unavoidable activity in software development. Various approaches and techniques have been explored in the literature to support code search tasks. Most of these approaches focus on serving user queries provided as natural language free-form input. However, there exists a wide range of use-case scenarios where a code-to-code approach would be most beneficial. For example, research directions in code transplantation, code diversity, patch recommendation can leverage a code-to-code search engine to find essential ingredients for their techniques. In this paper, we propose FaCoY, a novel approach for statically finding code fragments which may be semantically similar to user input code. FaCoY implements a query alternation strategy: instead of directly matching code query tokens with code in the search space, FaCoY first attempts to identify other tokens which may also be relevant in implementing the functional behavior of the input code. With various experiments, we show that (1) FaCoY is more effective than online code-to-code search engines; (2) FaCoY can detect more semantic code clones (i.e., Type-4) in BigCloneBench than the state-of-the-art; (3) FaCoY, while static, can detect code fragments which are indeed similar with respect to runtime execution behavior; and (4) FaCoY can be useful in code/patch recommendation.
Environmental complexity affects contextual fear conditioning following hippocampal lesions in rats

Contextual fear conditioning has become a benchmark measure for hippocampal function, even though several studies report successful acquisition in hippocampal‐damaged rodents. The current study examined whether environmental complexity may account for these discrepancies. We directly compared single‐session contextual fear conditioning in rats in a simple vs. complex environment. Hippocampal lesions led to reduced fear conditioning in both contexts, as measured by freezing, but the effect was significantly greater in the complex context. As well, lesions led to generalized fear when the complex context was paired with shock, but not when the simple context was paired. We suggest that the representation of the simple context formed by rats with hippocampal lesions was adequate to support associative learning, but the representation of the complex context, which depended to a greater extent on relational learning, was not. The results were interpreted as consistent with theories of hippocampal function that emphasize its role in integrating multiple stimulus elements in a memory trace. © 2007 Wiley‐Liss, Inc.
Different Patterns of Autobiographical Memory Loss in Semantic Dementia and Medial Temporal Lobe Amnesia: a Challenge to Consolidation Theory.

Temporally graded retrograde memory loss, with a disproportionate impairment of recent relative to remote memories, is considered a hallmark of medial temporal lobe amnesia. According to consolidation theory, the hippocampal complex, which includes the hippocampal formation, parahippocampal gyrus, the entorhinal and perirhinal cortex, plays a time-limited role in memory, needed only until consolidation in the neocortex is complete (Squire, Psychological Review 1992; 99: 195–231). Recent support for this theory comes from findings of a reverse gradient in people with semantic dementia with neocortical degeneration but a relatively preserved hippocampal complex (Hodges and Graham, Neuropsychologia 1998; 36: 803–25). Consolidation theory is challenged by evidence that remote autobiographical memory is not always spared in amnesia (Nadel and Moscovitch, Current Opinion in Neurobiology 1997; 7: 217–27) and that semantic memory becomes highly personalized in semantic dementia (Snowden et al., Memory 1995; 3: 225–46). According to Nadel and Moscovitch, the hippocampal complex is needed to retain and retrieve detailed memories of autobiographical episodes no matter how old they are. To test consolidation theory against the opposing view, we investigated the role of the hippocampal complex in recent and remote autobiographical and personal semantic memory by contrasting the memory of a semantic dementia patient, EL, with that of an amnesic patient, KG, using family photographs as recall cues. KG demonstrated a complete loss of autobiographical episodes with a sparing of autobiographical facts; EL demonstrated well-preserved memory for episodes with a reverse gradient for personally relevant names. The influence of autobiographical significance on memory for names of public figures was examined further by comparing the effect that familiarity and recollection had on recognition of names of famous people and famous places. EL’s memory was influenced by autobiographical significance, whereas KC’s was not. We propose that the hippocampal complex plays a permanent role in the storage and retrieval of autobiographical episodes and that autobiographical significance may affect semantic representations.
ON FELLER SEMIGROUPS ASSOCIATED WITH ONE-DIMENSIONAL DIFFUSION PROCESSES WITH MEMBRANES

By analytical method we obtain the integral representation of a two-parameter semigroup of operators associated with Feller process on a line which is a result of pasting together given diffusions at finite number of fixed points. The behavior of this process at each point of pasting together is described by Feller-Wentzell conjugation condition containing the integral term (nonlocal component).
Effect of solidification velocity on weld solidification process of alloy tool steel

In order to clarify the effect of solidification velocity on the weld solidification process of alloy tool steel during the welding, the information about microstructure evolution was obtained by the concurrent experiments of liquid tin quenching and time resolved X-ray diffraction technique using intense synchrotron radiation. It was found from the experiments that the solidification mode was transferred from an FA to an A mode at the high solidification velocity. The effect of solidification velocity on the phase selection during solidification between the primary δ-ferrite and γ-austenite was theoretically proved by the Kurz, Giovanola and Trivedi (KGT) model. It is thus explained that the solidification cracking susceptibility of the weld metal of alloy tool steel was enhanced due to the δ to γ transition of the primary phase.
The 1986-1989 ENSO cycle in a chemical climate model

A pronounced ENSO cycle occurred from 1986 to 1989, accompanied by distinct dynamical and chemical anomalies in the global troposphere and stratosphere. Reproducing these effects with current climate models not only provides a model test but also contributes to our still limited understanding of ENSO's effect on stratosphere-troposphere coupling. We performed several sets of ensemble simulations with a chemical climate model (SOCOL) forced with global sea surface temperatures. Results were compared with observations and with large-ensemble simulations performed with an atmospheric general circulation model (MRF9). We focus our analysis on the extratropical stratosphere and its coupling with the troposphere. In this context, the circulation over the North Atlantic sector is particularly important. Relative to the La Nina winter 1989, observations for the El Nino winter 1987 show a negative North Atlantic Oscillation index with corresponding changes in temperature and precipitation patterns, a weak polar vortex, a warm Arctic middle stratosphere, negative and positive total ozone anomalies in the tropics and at middle to high latitudes, respectively, as well as anomalous upward and poleward Eliassen-Palm (EP) flux in the midlatitude lower stratosphere. Most of the tropospheric features are well reproduced in the ensemble means in both models, though the amplitudes are underestimated. In the stratosphere, the SOCOL simulations compare well with observations with respect to zonal wind, temperature, EP flux, meridional mass streamfunction, and ozone, but magnitudes are underestimated in the middle stratosphere. With respect to the mechanisms relating ENSO to stratospheric circulation, the results suggest that both, upward and poleward components of anomalous EP flux are important for obtaining the stratospheric signal and that an increase in strength of the Brewer-Dobson circulation is part of that signal.
The Will to Improve: Governmentality, Development, and the Practice of Politics

This Book Review is brought to you for free and open access by the Anthropology at Scholar Commons. It has been accepted for inclusion in Journal of Ecological Anthropology by an authorized editor of Scholar Commons. For more information, please contact scholarcommons@usf.edu. Recommended Citation Sabogal, Mabel. "The Will to Improve: Governmentality, Development, and the Practice of Politics. " Journal of Ecological Anthropology 13, no. 1 (2009): 78-80.
Long-Term Effects of Pre-Placement Risk Factors on Children’s Psychological Symptoms and Parenting Stress Among Families Adopting Children From Foster Care

This exploratory longitudinal study examined behavioral outcomes and parenting stress among families with children adopted from foster care, taking into account environmental and biological risk factors. Child internalizing and externalizing problems and parenting stress were assessed in 82 adopted children and their families at 2 months post-placement, 12 months post-placement, and then yearly until 5 years post-placement. A history of abuse/neglect predicted significantly higher externalizing and internalizing problems at a borderline level of statistical significance. In the initial stages after placement, externalizing problems were significantly higher among children who were 4 years or older at placement versus those who were younger than 4, although differences were no longer significant 5 years post-placement. Statistical trends in parenting stress reflected reduced stress in the first 12 months followed by a plateau for parents who adopted older children and greater stress for parents who adopted younger children. Familiar limitations for observational cohort data apply. Nonetheless, the availability of longitudinal follow-up on a sizable sample of children adopted from foster care adds insight to the psychological dynamics for adoptive families and suggests that families of children adopted from the foster care system may have unique needs for ongoing support around behavioral issues.
Chapter 2 Requirements for an artificial intervertebral disc

Intervertebral disc degeneration is an important social and economical problem. Presently available artificial intervertebral discs (AIDs) are insufficient and the main surgical intervention is still spinal fusion. The objective of the present study is to present a list of requirements for the development of an AID which could replace the human lumbar intervertebral disc and restores its function. The list addresses geometry, stiffness, range of motion, strength, facet joint function, center of rotation, fixation, failsafety and implantation technique. Date are obtained from literature, quantified where possible and checked for consistency. Existing AIDs are evaluated according to the presented list of requirements. Endplate size is a weak point in existing AIDs. These should be large and fit vertebral bodies to prevent migration. Disc height and wedge angle should be restored, unless this would overstretch ligaments. Finally, stiffness and range of motion in all directions should equal those of the healthy disc, except for the axial rotation to relieve the facet joints. (Int J Artif Organs 2001; 24: 311-21)
Clinical and echocardiographic response of apical vs nonapical right ventricular lead position in CRT: A meta‐analysis

Traditionally the right ventricular (RV) pacing lead is placed in the RV apex in cardiac resynchronization therapy (CRT). It is not clear whether nonapical placement of the RV lead is associated with a better response to CRT. We aimed to perform a meta‐analysis of all randomized controlled trials (RCTs) that compared apical and nonapical RV lead placement in CRT.
Clinical performance of bonded ceramic inlays/onlays: A 5- to 18-year retrospective longitudinal study.

PURPOSE This retrospective longitudinal study evaluated the clinical performance of bonded ceramic inlays/onlays, placed by the first author in his private practice, in a 5 to 18-year period. METHODS The patients evaluated had been treated in the office for at least 7 years and were still in the practice up to year 2013. 130 randomly selected patients agreed to participate in the study. 93 bonded ceramic inlays/onlays (BCRs), were placed on posterior teeth in 47 subjects. Gender, age, tooth preparation, number, type, extent, location, quality and survival of the restorations, ceramic materials, luting resins cements, parafunctional habits, secondary caries and maintenance therapy were the variables evaluated. Cohen 's Kappa coefficient, on the quality analysis of the restorations, ranged from 0.78 to 1. Fisher 's exact test, Chi Square test, Kruskal-Wallis test and Mann-Whitney non-parametric test were indicated to analyze significant differences. RESULTS At the initial examination, 87 (93.5%) restorations were in function and six failed (6.5%). 81 (93%) were rated as clinical successes. The observed mean survival time of those that remained functional was 11 years. The standard deviation was 4 years, with a 95% CI for the overall observed mean survival time (10 years-11 years, 9 months). 87 of 93 BCRs had a functional success of 93.5%, with an observed mean survival of 11 years. The clinical performance of bonded ceramic onlays was very acceptable. CLINICAL SIGNIFICANCE Bonded ceramic onlays showed a predictable, esthetic, and functional treatment, with acceptable longevity.
Conserved amino acid networks involved in antibody variable domain interactions

Engineered antibodies are a large and growing class of protein therapeutics comprising both marketed products and many molecules in clinical trials in various disease indications. We investigated naturally conserved networks of amino acids that support antibody VH and VL function, with the goal of generating information to assist in the engineering of robust antibody or antibody‐like therapeutics. We generated a large and diverse sequence alignment of V‐class Ig‐folds, of which VH and VL domains are family members. To identify conserved amino acid networks, covariations between residues at all possible position pairs were quantified as correlation coefficients (ϕ‐values). We provide rosters of the key conserved amino acid pairs in antibody VH and VL domains, for reference and use by the antibody research community. The majority of the most strongly conserved amino acid pairs in VH and VL are at or adjacent to the VH–VL interface suggesting that the ability to heterodimerize is a constraining feature of antibody evolution. For the VH domain, but not the VL domain, residue pairs at the variable‐constant domain interface (VH–CH1 interface) are also strongly conserved. The same network of conserved VH positions involved in interactions with both the VL and CH1 domains is found in camelid VHH domains, which have evolved to lack interactions with VL and CH1 domains in their mature structures; however, the amino acids at these positions are different, reflecting their different function. Overall, the data describe naturally occurring amino acid networks in antibody Fv regions that can be referenced when designing antibodies or antibody‐like fragments with the goal of improving their biophysical properties. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Nitrification and growth of autotrophic nitrifying bacteria and Thaumarchaeota in the coastal North Sea

Nitrification and the associated growth of autotrophic nitrifiers, as well as the contributions of bacteria and Thaumarchaeota to total autotrophic C-fixation by nitrifiers were investigated in the Dutch coastal North Sea from October 2007 to March 2008. Rates of nitrification were determined by incubation of water samples with 15 N-ammonium and growth of autotrophic nitrifiers was measured by incubation with 13 C-DIC (dissolved inorganic carbon) in the presence and absence of nitrification inhibitors (nitrapyrin and chlorate) in combination with compound-specific stable isotope ( 13 C) analysis of bacterial and Thaumarchaeotal lipid biomarkers. Net nitrification during the sampling period was evident from the concentration dynamics of ammonium, nitrite and nitrate. Measured nitrification rates were high (41–221 nmol N L −1 h −1 ). Ammonium assimilation was always substantially lower than nitrification – with nitrification on average contributing 89% (range 73–97%) to total ammonium consumption. 13 C-DIC fixation into bacterial and Thaumarchaeotal lipids was strongly reduced by the nitrification inhibitors (27–95 %). The inhibitor-sensitive 13 C-PLFA (phospholipid-derived fatty acid) pool was dominated by the common PLFAs 16:0, 16:1ω7c and 18:1ω7c throughout the whole sampling period and occasionally also included the polyunsaturated fatty acids 18:2ω6c and 18:3ω3. 13 C-DIC fixation activity of the nitrifying bacteria was much higher than that of the nitrifying Thaumarchaeota throughout the whole sampling period, even during the peak in Thaumarchaeotal abundance and activity. This suggests that the contribution of autotrophic Thaumarchaeota to nitrification during winter in the coastal North Sea may have been smaller than expected from their gene abundance (16S rRNA and amoA (ammonia monooxygenase)). These results emphasize the importance of direct measurements of the actual activity of bacteria and Thaumarchaeota, rather than abundance measurements only, in order to elucidate their biogeochemical importance. The ratio between rates of nitrification versus DIC fixation by bacterial nitrifiers was higher or even much higher than typical values for autotrophic nitrifiers, indicating that little DIC was fixed relative to the amount of energy that was generated by nitrification.