Miracle-dz/UniFAR-FTUs huggingface dataset:
Co‐occurrence of genes for aerobic and anaerobic biodegradation of dichloroethane in organochlorine‐contaminated groundwater

ABSTRACT 1,2‐Dichloroethane (DCA) is a problematic groundwater pollutant. Factors influencing the distribution and activities of DCA‐degrading bacteria are not well understood, which has hampered their application for bioremediation. Here, we used quantitative PCR to investigate the distribution of putative DCA‐dehalogenating bacteria at a DCA‐impacted site in Sydney (Australia). The dehalogenase genes dhlA, tceA and bvcA were detected in all groundwater samples (n = 15), while vcrA was found in 11/15 samples. The 16S rRNA gene sequences specific to the dehalogenating genera Dehalobacter, Desulfitobacterium and Dehalogenimonas were detected in 15/15, 13/15 and 13/15 samples, respectively, while Dehalococcoides sequences were found in 9/15 samples. The tceA, bvcA and vcrA genes occurred in the same samples as Dehalococcoides and Dehalobacter. Microcosm experiments confirmed the presence of bacteria capable of dechlorination under anoxic conditions. The abundance of the dhlA gene, which is found in hydrolytic DCA degraders, was positively correlated to the DCA concentration, and was unexpectedly most abundant in samples with low oxygen conditions. A dhlA‐containing bacterium isolated from the site (Xanthobacter EL8) was capable of anaerobic growth on DCA under denitrifying conditions. The presence of diverse DCA‐dehalogenating bacteria at this site indicates that natural attenuation or biostimulation could be valid approaches for site cleanup.
UvA-DARE ( Digital Academic Repository ) Positive and negative early life experiences differentially modulate long term survival and amyloid protein levels in a mouse model of Alzheimer ’ s disease

Stress has been implicated as a risk factor for the severity and progression of sporadic Alzheimer’s disease (AD). Early life experiences determine stress responsivity in later life, and modulate age-dependent cognitive decline. Therefore, we examined whether early life experiences influence AD outcome in a bigenic mouse model which progressively develops combined tau and amyloid pathology (biAT mice). Mice were subjected to either early life stress (ELS) or to ‘positive’ early handling (EH) postnatally (from day 2 to 9). In biAT mice, ELS significantly compromised long term survival, in contrast to EH which increased life expectancy. In 4 month old mice, ELS-reared biAT mice displayed increased hippocampal Aβ levels, while these levels were reduced in EH-reared biAT mice. No effects of ELS or EH were observed on the brain levels of APP, protein tau, or PSD-95. Dendritic morphology was moderately affected after ELS and EH in the amygdala and medial prefrontal cortex, while object recognition memory and open field performance were not affected. We conclude that despite the strong transgenic background, early life experiences significantly modulate the life expectancy of biAT mice. Parallel changes in hippocampal Aβ levels were evident, without affecting cognition of young adult biAT mice.
The association of serum 25-hydroxyvitamin D3 and D2 with depressive symptoms in childhood – a prospective cohort study

Background Depression in adolescence is common and early onset predicts worse outcome in adulthood. Studies in adults have suggested a link between higher total 25-hydroxyvitamin D [25(OH)D] concentrations and lower risk of depression. Objectives To investigate (a) the association between serum 25(OH)D2 and 25(OH)D3 concentrations and depressive symptoms in children, and (b) whether the associations of 25(OH)D2 and 25(OH)D3 are different from, and independent of, each other. Methods Prospective cohort study with serum 25(OH)D2 and 25(OH)D3 concentrations measured at mean age of 9.8 years and depressive symptoms assessed with the Mood and Feelings Questionnaire by a trained interviewer at the mean ages of 10.6 years (n = 2,759) and 13.8 years (n = 2,752). Results Higher concentrations of 25(OH)D3 assessed at mean age 9.8 years were associated with lower levels of depressive symptoms at age 13.8 years [adjusted risk ratio (RR; 95% confidence interval (CI)): 0.90 (0.86–0.95)], but not at age 10.6 years [adjusted RR (95% CI): 0.98 (0.93–1.03)] and with increased odds of decreasing symptoms between age 10.6 and 13.8 years [adjusted RR (95% CI): 1.08 (1.01–1.16)]. Serum 25(OH)D2 concentrations were not associated with depressive symptoms. Conclusions This is the first study in children to suggest that the association between 25(OH)D3 concentrations and depression emerges in childhood. The association is independent of a wide range of potential confounding factors, and appears to be stronger with greater time separation between assessment of 25(OH)D3 and assessment of depressive symptoms. Confirmation of our findings in large prospective studies and trials would be valuable.
Perceptual Representation Systems and Implicit Memory

Consider the following experimental situations. In the first, subjects are shown a list of familiar words and are instructed to carefully study each of them. After performing a variety of unrelated tasks for several minutes, they are told to think back to the study list and recall as many of the presented words as possible. Subjects are then shown a series of words-half were presented in the study list, half were not-and are instructed to say “yes” if they remember having studied the items, and “no” if they do not remember them. In the second situation, subjects also study a word list and then engage in unrelated activities for a few minutes. However, instead of then being asked to remember previously studied items, the subjects are asked to write down the first word that comes to mind in response to a series of 3-letter word stems; some can be completed with previously studied words, and some cannot. The first of these two hypothetical situations reflects the way in which cognitive psychologists have traditionally studied human memory: by assessing subjects’ intentional or explicit memoy for information acquired during a study episode with standard recall and recognition tests. In the second situation, memory is inferred from an enhanced tendency to complete 3-letter stems with previously studied words; this is often referred to as “repetition priming” or “direct priming” (cf., Cofer, 1967; Tulving & Schacter, 1990). Priming effects need not and often do not involve any conscious or explicit recollection of a prior episode, and thus can be said to reflect implicit memory for previously studied information (Graf & Schacter, 1985; Schacter, 1987). Priming has been assessed with a variety of implicit memory tasks that do not require explicit recollection of a specific prior episode. One common type of implicit test involves completing word stems or word fragments with the first word that comes to mind, as in the foregoing example (e.g., Graf & Mandler, 1984; Light, Singh & Capps, 1986; Roediger & Blaxton, 1987a, b; Schacter & Graf, 1986a, b; Tulving, Schacter & Stark, 1982). Another frequently used implicit task involves word identification: Subjects are required to try to identify a word from a brief (e.g., 50-msec) perceptual exposure, and priming is indicated by more accurate identification of a recently studied item than of a new, nonstudied item (e.g., Jacoby, 1983a, b;
IL-21 Is an Antitolerogenic Cytokine of the Late-Phase Alloimmune Response

OBJECTIVE Interleukin-21 (IL-21) is a proinflammatory cytokine that has been shown to affect Treg/Teff balance. However, the mechanism by which IL-21 orchestrates alloimmune response and interplays with Tregs is still unclear. RESEARCH DESIGN AND METHODS The interplay between IL-21/IL-21R signaling, FoxP3 expression, and Treg survival and function was evaluated in vitro in immunologically relevant assays and in vivo in allogenic and autoimmune models of islet transplantation. RESULTS IL-21R expression decreases on T cells and B cells in vitro and increases in the graft in vivo, while IL-21 levels increase in vitro and in vivo during anti-CD3/anti-CD28 stimulation/allostimulation in the late phase of the alloimmune response. In vitro, IL-21/IL-21R signaling (by using rmIL-21 or genetically modified CD4+ T cells [IL-21 pOrf plasmid–treated or hIL-21-Tg mice]) enhances the T-cell response during anti-CD3/anti-CD28 stimulation/allostimulation, prevents Treg generation, inhibits Treg function, induces Treg apoptosis, and reduces FoxP3 and FoxP3-dependent gene transcripts without affecting FoxP3 methylation status. In vivo targeting of IL-21/IL-21R expands intragraft and peripheral Tregs, promotes Treg neogenesis, and regulates the antidonor immune response, whereas IL-21/IL-21R signaling in Doxa-inducible ROSA-rtTA-IL-21-Tg mice expands Teffs and FoxP3− cells. Treatment with a combination of mIL-21R.Fc and CTLA4-Ig (an inhibitor of the early alloimmune response) leads to robust graft tolerance in a purely alloimmune setting and prolonged islet graft survival in NOD mice. CONCLUSIONS IL-21 interferes with different checkpoints of the FoxP3 Treg chain in the late phase of alloimmune response and, thus, acts as an antitolerogenic cytokine. Blockade of the IL-21/IL-21R pathway could be a precondition for tolerogenic protocols in transplantation.
Effect of Polystyrene Addition on Freeze Casting of Ceramic/Camphene Slurry for Ultra‐High Porosity Ceramics with Aligned Pore Channels

We investigated the effect of polystyrene (PS) addition on the freezing behavior of a very dilute alumina/camphene slurry with an initial solid loading of 5 vol% for the fabrication of ultra-high porosity ceramics with aligned pore channels. To accomplish this, slurries with various PS contents (10, 20, and 30 vol% in relation to the alumina powders) were prepared by ball milling at 60°C and then cast into molds at a constant temperature of 20°C. After removing the frozen camphene, the samples were heat treated to burn out the organic phases and sinter the alumina walls. The addition of the PS binder remarkably enhanced the green strength of the sample, making it possible to handle it without difficulty. All of the sintered samples showed ultra-high porosities of >88% without the collapse of the porous structure, wherein the pore channels were completely interconnected. Three distinctive zones having different pore structures were observed, viz. the outer shell with elongated pores, the inner zone with long aligned pore channels, and the center with equiaxed pores. The content of the PS polymer significantly affected the pore morphologies in the three distinctive zones. In addition, it was found that the addition of the PS polymer was highly beneficial to the alignment of the pore channels.
Isolation and Identification of Compounds from Bioactive Extracts of Taraxacum officinale Weber ex F. H. Wigg. (Dandelion) as a Potential Source of Antibacterial Agents

Currently, the most effective treatment for recurrent urinary tract infections in women is antibiotics. However, the limitation for this treatment is the duration and dosage of antibiotics and the resistance that bacteria develop after a long period of administration. With the aim of identifying mainly novel natural agents with antibacterial activity, the present study was undertaken to investigate the biological and phytochemical properties of extracts from the leaves Taraxacum officinale. The structural identification of compounds present in hexane (Hex) and ethyl acetate (AcOEt) extracts was performed by mass spectrometry (GC-MS) spectroscopic techniques and nuclear magnetic resonance (NMR) with the major compounds corresponding to different sesquiterpene lactones (α-santonin, glabellin, arborescin, and estafiatin), monoterpene (9,10-dimethyltricycle [4.2.1.1 (2,5)]decane-9,10-diol), phytosterol (Stigmasta-5,22-dien-3β-ol acetate), terpenes (lupeol acetate, pregn-5-en-20-one-3β-acetyloxy-17-hydroxy, 2-hydroxy-4-methoxy benzaldehyde), and coumarin (benzofuranone 5,6,7,7-a-tetraaldehyde-4,4,7a-trimethyl). The results obtained show that the Hex extract was highly active against Staphylococcus aureus showing a MIC of 200 μg/mL and moderately active against Escherichia coli and Klebsiella pneumoniae with MIC values of 400 μg/mL and 800 μg/mL for the other Gram-negative strains tested with Proteus mirabilis as uropathogens in vitro. Therefore, the effective dandelion extracts could be used in the development of future products with industrial application.
Parsing profiles of temperamental reactivity and differential routes to delay of gratification: A person-based approach

Abstract Informed by a developmental psychopathology perspective, the present study applied a person-based approach to examine whether associations between early sociocontextual experiences (e.g., socioeconomic factors and maternal discipline practices) and preschool-age children's delay of gratification vary across profiles of children's temperamental reactivity. In addition, the study examined the direct and mediating role of children's set shifting in associations with delay of gratification within each profile. The sample consisted of 160 socioeconomically and ethnically diverse mothers and their 5-year-old children drawn from a longitudinal study of mother–child relationships. Latent profile analyses identified three profiles of temperamental reactivity distinguished by sensitivity to reward and punishment and negative affectivity. Multigroup analysis revealed maternal sensitive discipline (observed during a parent–child compliance task) at age 3.5 predicted longer delay of gratification at age 5 in the punishment reactivity/negative affectivity group. Maternal inductive reasoning discipline at age 3.5 predicted longer delay in the low temperamental reactivity group. For children with the reward reactivity/negative affectivity profile, higher family income at age 3.5 predicted longer delay of gratification at age 5, which was mediated by children's set shifting. Findings underscore the utility of person-based approaches for delineating differential developmental routes toward children's delay of gratification.
The Role of Organizational Control Systems in Employees’ Organizational Trust and Performance Outcomes

This study examined how organizational control is related to employees’ organizational trust. We specifically focus on how different forms of control (process, outcome, and normative) relate to employees’ trust in their employing organizations and examine whether such trust in turn relates positively to employee job performance (task performance and organizational citizenship behavior). In addition, and in response to the recommendations of past research, we examined these relationships in a high control and compliance-based cultural context. Using data from 105 employee–supervisor dyads from professional services firms in Singapore, we find support for our hypothesized model. The implications of the results for theory and practice, and directions for future research, are discussed.
The Ever-Evolving Concept of the Cancer Stem Cell in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC), the most common type of pancreatic cancer, is the 4th most frequent cause of cancer-related death worldwide, primarily due to the inherent chemoresistant nature and metastatic capacity of this tumor. The latter is believed to be mainly due to the existence of a subpopulation of highly plastic “stem”-like cells within the tumor, known as cancer stem cells (CSCs), which have been shown to have unique metabolic, autophagic, invasive, and chemoresistance properties that allow them to continuously self-renew and escape chemo-therapeutic elimination. As such, current treatments for the majority of PDAC patients are not effective and do not significantly impact overall patient survival (<7 months) as they do not affect the pancreatic CSC (PaCSC) population. In this context, it is important to highlight the need to better understand the characteristics of the PaCSC population in order to develop new therapies to target these cells. In this review, we will provide the latest updates and knowledge on the inherent characteristics of PaCSCs, particularly their unique biological properties including chemoresistance, epithelial to mesenchymal transition, plasticity, metabolism and autophagy.
Body Mass Index, Falls, and Hip Fractures Among Nursing Home Residents

Background To examine the association between body mass index (BMI) and the risk for falls and hip fractures among nursing home (NH) residents. Methods A cohort study of newly admitted NH residents, excluding those with a prior history of hip fracture. Using the Minimum Data Set 2.0 (2006-2010), we determined the occurrence of new falls and hip fractures among NH residents during their first 3 months of stay. Residents were categorized as underweight (BMI < 18.5), normal-to-overweight (18.5 ≤ BMI < 30), mildly obese (30 ≤ BMI < 35), and moderately-to-severely obese (BMI ≥ 35). Results Among newly admitted NH residents over the first 3 months, 51.1% of underweight residents, 53.1% of normal-to-overweight residents, 49.1% of residents with mild obesity, and 43.1% of residents with moderate-to-severe obesity experienced a fall; 3.1% of underweight residents, 2.5% of normal-to-overweight residents, 1.5% of residents with mild obesity, and 1.1% of residents with moderate-to-severe obesity experienced a hip fracture. In comparison with normal-to-overweight residents, after adjustment for resident-level and facility-level characteristics, mildly obese residents (odds ratio [OR] = 0.94, 95% confidence interval [CI] = [0.91-0.93]), and moderately-to-severely obese residents (OR = 0.84 [95% CI = 0.83-0.85]) were less likely to experience a fall; Mildly obese residents (OR = 0.65 [95% CI = 0.63-0.68]), and moderately-to-severely obese residents (OR = 0.84 [95% CI = 0.83-0.85]) were less likely, and underweight residents were more likely (OR = 1.22 [95% CI = 1.18-1.26]) to experience a hip fracture. Conclusion Obesity is associated with reduced risks for falls and hip fractures among newly admitted NH residents. Future studies are needed to explore possible explanations for these associations.
Pupillometry reveals perceptual differences that are tightly linked to autistic traits in typical adults

The pupil is primarily regulated by prevailing light levels but is also modulated by perceptual and attentional factors. We measured pupil-size in typical adult humans viewing a bistable-rotating cylinder, constructed so the luminance of the front surface changes with perceived direction of rotation. In some participants, pupil diameter oscillated in phase with the ambiguous perception, more dilated when the black surface was in front. Importantly, the magnitude of oscillation predicts autistic traits of participants, assessed by the Autism-Spectrum Quotient AQ. Further experiments suggest that these results are driven by differences in perceptual styles: high AQ participants focus on the front surface of the rotating cylinder, while those with low AQ distribute attention to both surfaces in a more global, holistic style. This is the first evidence that pupillometry reliably tracks inter-individual differences in perceptual styles; it does so quickly and objectively, without interfering with spontaneous perceptual strategies.
The menstrual cycle affects recognition of emotional expressions: an event-related potential study

Background: Several studies have investigated the relationship between behavioral changes and the menstrual cycle in female subjects at a reproductive age. The present study investigated the relationship between the menstrual cycle and emotional face recognition by measuring the N170 component of ERPs. Methods: We measured N170 of twelve women in both follicular phase and late luteal phase who were presented with human facial expressions as stimuli (happy and angry). Results: In the follicular phase, participants showed a significantly larger response to happy male facial expressions. In the late luteal phase, participants had longer reaction times to all emotional stimuli, and a significantly reduced response to happy faces, especially happy male facial expressions (P<0.001). Conclusions: Our findings suggest that the menstrual cycle modulates early visual cognitive processing, and highlight the importance of considering the menstrual cycle phase in studies that investigate emotion and cognition.
Depression in Mexican Americans with diagnosed and undiagnosed diabetes

Background Depression and diabetes commonly co-occur; however, the strength of the physiological effects of diabetes as mediating factors towards depression is uncertain. Method We analyzed extensive clinical, epidemiological and laboratory data from n = 2081 Mexican Americans aged 35–64 years, recruited from the community as part of the Cameron County Hispanic Cohort (CCHC) divided into three groups: Diagnosed (self-reported) diabetes (DD, n = 335), Undiagnosed diabetes (UD, n = 227) and No diabetes (ND, n = 1519). UD participants denied being diagnosed with diabetes, but on testing met the 2010 American Diabetes Association and World Health Organization definitions of diabetes. Depression was measured using the Center for Epidemiological Studies – Depression (CES-D) scale. Weighted data were analyzed using dimensional and categorical outcomes using univariate and multivariate models. Results The DD group had significantly higher CES-D scores than both the ND and UD (p ⩽ 0.001) groups, whereas the ND and UD groups did not significantly differ from each other. The DD subjects were more likely to meet the CES-D cut-off score for depression compared to both the ND and UD groups (p = 0.001), respectively. The UD group was also less likely to meet the cut-off score for depression than the ND group (p = 0.003). Our main findings remained significant in models that controlled for socio-demographic and clinical confounders. Conclusions Meeting clinical criteria for diabetes was not sufficient for increased depressive symptoms. Our findings suggest that the ‘knowing that one is ill’ is associated with depressive symptoms in diabetic subjects.
IL‐4 drives microglia and macrophages toward a phenotype conducive for tissue repair and functional recovery after spinal cord injury

Macrophages and microglia play a key role in the maintenance of nervous system homeostasis. However, upon different challenges, they can adopt several phenotypes, which may lead to divergent effects on tissue repair. After spinal cord injury (SCI), microglia and macrophages show predominantly pro‐inflammatory activation and contribute to tissue damage. However, the factors that hamper their conversion to an anti‐inflammatory state after SCI, or to other protective phenotypes, are poorly understood. Here, we show that IL‐4 protein levels are undetectable in the spinal cord after contusion injury, which likely favors microglia and macrophages to remain in a pro‐inflammatory state. We also demonstrate that a single delayed intraspinal injection of IL‐4, 48 hours after SCI, induces increased expression of M2 marker in microglia and macrophages. We also show that delayed injection of IL‐4 leads to the appearance of resolution‐phase macrophages, and that IL‐4 enhances resolution of inflammation after SCI. Interestingly, we provide clear evidence that delayed administration of IL‐4 markedly improves functional outcomes and reduces tissue damage after contusion injury. It is possible that these improvements are mediated by the presence of macrophages with M2 markers and resolution‐phase macrophages. These data suggest that therapies aimed at increasing IL‐4 levels could be valuable for the treatment of acute SCI, for which there are currently no effective treatments. GLIA 2016;64:2079–2092