Miracle-dz/UniFAR-FTUs huggingface dataset:
OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities

Microorganisms rarely live isolated in their natural environments but rather function in consolidated and socializing communities. Despite the growing availability of high-throughput sequencing and metagenomic data, we still know very little about the metabolic contributions of individual microbial players within an ecological niche and the extent and directionality of interactions among them. This calls for development of efficient modeling frameworks to shed light on less understood aspects of metabolism in microbial communities. Here, we introduce OptCom, a comprehensive flux balance analysis framework for microbial communities, which relies on a multi-level and multi-objective optimization formulation to properly describe trade-offs between individual vs. community level fitness criteria. In contrast to earlier approaches that rely on a single objective function, here, we consider species-level fitness criteria for the inner problems while relying on community-level objective maximization for the outer problem. OptCom is general enough to capture any type of interactions (positive, negative or combinations thereof) and is capable of accommodating any number of microbial species (or guilds) involved. We applied OptCom to quantify the syntrophic association in a well-characterized two-species microbial system, assess the level of sub-optimal growth in phototrophic microbial mats, and elucidate the extent and direction of inter-species metabolite and electron transfer in a model microbial community. We also used OptCom to examine addition of a new member to an existing community. Our study demonstrates the importance of trade-offs between species- and community-level fitness driving forces and lays the foundation for metabolic-driven analysis of various types of interactions in multi-species microbial systems using genome-scale metabolic models.
Suicides in Visually Impaired Persons: A Nation-Wide Register-Linked Study from Finland Based on Thirty Years of Data

Focusing on seasonality, gender, age, and suicide methods a Finnish nation-wide cohort-based study was carried out to compare suicide data between sighted, visually-impaired (WHO impairment level I-II, i.e., visual acuity >0.05, but <0.3) and blind (WHO impairment level III-V, i.e., visual acuity <0.05) victims. Standardized mortality ratios (SMR) of age- and gender-matched populations from official 1982–2011 national registers were used. Group differences in categorical variables were assessed with Pearson's Chi-square or Fisher's Exact test and in continuous variables with Mann-Whitney U-test. Seasonality was assessed by Chi-square for multinomials; ratio of observed to expected number of suicides was calculated with 95% confidence level. Hanging, poisoning, drowning, but rarely shooting or jumping from high places, were preferred suicide methods of the blind. Mortality was significantly increased in the visually impaired (SMR = 1.3; 95% CI 1.07–1.61), but in gender-stratified analyses the increase only affected males (1.34; 95% CI = 1.06–1.70) and not females (1.24; 95% CI 0.82–1.88). Age-stratified analyses identified blind males of working age rather than older men (as in the general population) as a high risk group that requires particular attention. The statistically significant spring suicide peak in blind subjects mirrors that of sighted victims and its possible cause in the blind is discussed.
Pairs of Vp1 Cysteine Residues Essential for Simian Virus 40 Infection

ABSTRACT Transient disulfide bonding occurs during the intracellular folding and pentamerization of simian virus 40 (SV40) major capsid protein Vp1 (P. P. Li, A. Nakanishi, S. W. Clark, and H. Kasamatsu, Proc. Natl. Acad. Sci. USA 99:1353-1358, 2002). We investigated the requirement for Vp1 cysteine pairs during SV40 infection. Our analysis identified three Vp1 double-cysteine mutant combinations that abolished viability as assayed by plaque formation. Mutating the Cys49-Cys87 pair or the Cys87-Cys254 pair led to ineffective nuclear localization and diminished accumulation of the mutant Vp1s, and the defect extended in a dominant-negative manner to the wild-type minor capsid proteins Vp2/3 and an affinity-tagged recombinant Vp1 expressed in the same cells. Mutating the Cys87-Cys207 pair preserved the nuclear localization and normal accumulation of the capsid proteins but diminished the production of virus-like particles. Our results are consistent with a role for Cys49, Cys87, and Cys254 in the folding and cytoplasmic-nuclear trafficking of Vp1 and with a role for Cys87 and Cys207 in the assembly of infectious particles. These findings suggest that transient disulfide bond formation between certain Vp1 cysteine residues functions at two stages of SV40 infection: during Vp1 folding and oligomerization in the cytoplasm and during virion assembly in the nucleus.
Bodily Experience in Schizophrenia: Factors Underlying a Disturbed Sense of Body Ownership

Emerging evidence is now challenging the view that patients diagnosed with schizophrenia experience a selective deficit in their sense of agency. Additional disturbances seem to exist in their sense of body ownership. However, the factors underlying this disturbance in body ownership remain elusive. Knowledge of these factors, and increased understanding of how body ownership is related to other abnormalities seen in schizophrenia, could ultimately advance development of new treatments. Research on body ownership in schizophrenia has mainly been investigated with the rubber hand illusion (RHI). Schizophrenia patients show higher susceptibility to the RHI, which may be explained by a stronger reliance on multisensory information over weaker stored body representations. This review shows that a coherent sense of body ownership arises from the integration of both bottom-up sensory processes and higher order, top-down bodily- and perceptual representations. Multisensory integration, temporal binding, anticipation, intention and efferent signals all partly modulate the complex experience of body ownership. Specifically, we propose that patients with schizophrenia have weaker stored body representations, and rely to a greater extent on external stimuli, such as visual information, due to imprecise or highly variable internal predictions. Moreover, the reduced sense of agency in schizophrenia may additionally contribute to the disturbed sense of body ownership, as evidence from healthy participants suggests that agency and body ownership are interrelated. Vice versa, a reduced sense of body ownership may also contribute to a reduced sense of agency. Future studies should explicitly target the precise relationship between the two in schizophrenia.
Input-Specific Modulation of Neurotransmitter Release in the Lateral Horn of the Spinal Cord via Adenosine Receptors

Activation of adenosine A2A receptors (A2ARs) in the CNS produces a variety of neuromodulatory actions dependent on the region and preparation examined. In autonomic regions of the spinal cord, A1R activation decreases excitatory synaptic transmission, but the effects of A2AR stimulation are unknown. We sought to determine the location and function of the A2ARs in the thoracic spinal cord, focusing on the intermediolateral cell column (IML). A2AR immunoreactivity was observed throughout the gray matter, with particularly dense immunostaining in regions containing sympathetic preganglionic neurons (SPNs), namely, the IML and intercalated nucleus. Electron microscopy revealed A2AR immunoreactivity within presynaptic terminals and in postsynaptic structures in the IML. To study the functional relevance of these A2ARs, visualized whole-cell patch-clamp recordings were made from electrophysiologically identified SPNs and interneurons within the IML. The A2AR agonist c2-[p-(carboxyethyl)phenethylamino]-5′-N-ethylcarboxyamidoadenosine (CGS 21680) had no significant effect on EPSPs but increased the amplitude of IPSPs elicited by stimulation of the lateral funiculus. These effects were attributable to activation of presynaptic A2ARs because CGS 21680 application altered the paired pulse ratio. Furthermore, neurons in the IML that have IPSPs increased via A2AR activation also receive excitatory inputs that are inhibited by A1R activation. These data show that activating A2ARs increase inhibitory but not excitatory transmission onto neurons in the IML. Simultaneous activation of A1Rs and A2ARs therefore could facilitate inhibition of the postsynaptic neuron, leading to an overall reduction of sympathetic nervous activity.
Association between Serum Irisin Levels and Non-Alcoholic Fatty Liver Disease in Health Screen Examinees

Irisin is a recently found myokine that aids obesity control and improves glucose homeostasis by acting on white adipose tissue cells and increases total energy consumption. The aim of this study was to evaluate serum irisin levels in patients with non-alcoholic fatty liver disease (NAFLD) and to compare these levels with those of normal controls. Among 595 health screen examinees who had visited our institute between January 2013 to March 2013, 355 patients (84 NAFLD patients and 271 normal controls) were enrolled depending on whether they gave written informed consents and their history of alcohol intake, blood tests, and abdominal ultrasonographic findings. Age; sex; laboratory test parameters; homeostasis model assessment-insulin resistance; and levels of leptin, adiponectin, and irisin were assessed. Serum irisin levels (ng/ml) were significantly higher in the NAFLD group than in normal controls (63.4±32.6 vs. 43.0±29.7, p<0.001) and higher in the mild fatty liver group than in the moderate-to-severe fatty liver group (68.3±38.2 vs. 56.6±21.2, p<0.001). Additionally, serum irisin levels were not different between the non-obese and obese groups (48.4±34.2 vs. 45.8±22.9, p = 0.492); however, the levels were significantly lowest in normal controls and highest in the mild fatty liver group in the non-obese (44.9±31.7 vs. 73.1±48.5 vs 59.7±18.0, p<0.001) and obese groups (35.0±17.0 vs. 62.9±21.2 vs. 54.6±23.3, p<0.001). Serum irisin levels were significantly higher in NAFLD patients, which is not consistent with the results of previously published studies. Therefore, more studies are needed to confirm the role of irisin in NAFLD.
Assessment of behavioral problems in dementia: the revised memory and behavior problems checklist.

The Revised Memory and Behavior Problems Checklist (RMBPC), a 24-item, caregiver-report measure of observable behavioral problems in dementia patients, provides 1 total score and 3 subscale scores for patient problems (memory-related, depression, and disruptive behaviors) and parallel scores for caregiver reaction. Data were obtained from 201 geriatric patients and their caregivers. Factor analysis confirmed 3 first-order factors, consistent with subscales just named, and 1 general factor of behavioral disturbance. Overall scale reliability was good, with alphas of . 84 for patient behavior and . 90 for caregiver reaction. Subscale alphas ranged from . 67 to . 89. Validity was confirmed through comparison of RMBPC scores with well-established indexes of depression, cognitive impairment, and caregiver burden. The RMBPC is recommended as a reliable and valid tool for the clinical and empirical assessment of behavior problems in dementia patients.
Does Using Social Networks Lead to Better Job Opportunities ? A Direct Test

Research on the effect of social networks on job search outcomes has provided mixed results. Some studies found that the use of social contacts has positive effects on wages and on the other indicators of job quality while some others found negative effects. Previous studies, however, suffered from several methodological limitations such as selecting on the dependent variable or ignoring unobserved heterogeneity. In this paper, I develop a novel empirical approach studying job search by shifting the attention from search outcomes to the search process. Specifically, I investigate the effect of using social ties on the quality of jobs to which job seekers apply. Using within-person fixed effects models, I show that when the job seeker uses social contacts, she applies to the jobs that require less education and pay less than the jobs to which she applies through formal methods. The results hold important implications for our understanding of the job search process and the role of social contacts within this process. Thesis Supervisor: Ofer Sharone Title: Mitsubishi Career Development Professor
Characterizing Novel Thermophilic Amylase Producing Bacteria From Taptapani Hot Spring, Odisha, India

Background: Amylases play a vital role in biotechnological studies and rank an important position in the world enzyme market (25% to 33%). Bioprocess method of amylase production is more effective than the other sources, since the technique is easy, cost effective, fast, and the enzymes of required properties can be procured. Objectives: The current study aimed to report the characteristics of novel amylase producing bacterial strains isolated from Taptapani hot spring, Odisha, India. Materials and Methods: Bacterial strains were isolated by dilution plating method from the water samples collected from Taptapani Hot Spring, Odisha and screened for amylase production through starch hydrolysis. The bacterial isolates were identified morphologically, biochemically, and finally by 16S rDNA profiling. Results: Based on the morphological, physiological, biochemical characteristics and the molecular characterization, the isolates SS1, SS2, and SS3 were identified as Bacillus barbaricus, Aeromonas veroni, and Stenotrophomonas maltophilia, respectively. The approximate molecular weight of enzymes from SS1, SS2, and SS3 strains were 19 kDa, 56 kDa and 49 kDa, respectively. Conclusions: The current report isolates, characterizes, and demonstrates the novel heat-adapted amylase-producing bacteria SS1, SS2 and SS3 from Taptapani hot spring, indicating its potentiality and stability under acidic conditions.
DWARV 2.0: A CoSy-based C-to-VHDL hardware compiler

In the last decade, a considerable amount of effort was spent on raising the implementation level of hardware systems by automatically extracting the parallelism from input applications and using tools to generate Hardware/Software co-design solutions. However, the tools developed thus far either focus on particular application domains or they impose severe restrictions on the input language. In this paper, we present the DWARV 2.0 compiler that accepts general C-code as input and generates synthesizable VHDL for unrestricted application domains. Dissimilar to previous hardware compilers, this implementation is based on CoSy compiler framework. This allowed us to build a highly modular compiler in which standard or custom optimizations can be easily integrated. Validation experiments showed speed-ups of up to 4.41× when comparing against another state of the art hardware compiler.
Comparative of early parenteral nutrition and late parenteral nutrition in preterm neonates.

Objective: To evaluate the differences and influences of early and late Parenteral Nutrition (PN) on preterm neonates. Methods: Retrospective study, which includes preterm neonates who were born and admitted to Neonatal Intensive Care Units (NICU), weighing under 2000 g and having received PN for more than 7 days. According to the timing of protein provision, divided into two groups-Early Parenteral Nutrition (EPN) and late parenteral nutrition (LPN). EPN is defined with a protein provision within 24 h of birth while LPN with a protein provision after 24 h of birth. The facts to examined include the day of weight gain (times to regain over birth weight), total days of PN, weight gain per day in grams (g), weights at discharge and days of hospitalization. Results: Among a 25 preterm neonates, 10 neonates received EPN while 15 received LPN. No statistical significance is found between the basic data of EPN and LPN. After the multiple regression analysis and correction of basic data’s between EPN and LPN, this study finds that the day of weight gain of EPN is earlier than that of LPN by about 0.41 day, weight gain per day in grams (g) and the weight at discharge of EPN are more than those of LPN by about 0.25 g and 0.27 g, respectively, and the total days of PN and the days of hospitalization in the NICU of EPN are more than those of LPN by about 0.15 day and 0.11 day respectively, however, none of the above is statistically significant. Conclusion: The results of this study show that early PN may provide the benefits to preterm neonates. No evidence is noted in blood urea blood urea nitrogen and creatinine level.
From User-Centered to Adoption-Centered Design: A Case Study of an HCI Research Innovation Becoming a Product

As we increasingly strive for scientific rigor and generalizability in HCI research, should we entertain any hope that by doing good science, our discoveries will eventually be more transferrable to industry? We present an in-depth case study of how an HCI research innovation goes through the process of transitioning from a university project to a revenue-generating startup financed by venture capital. The innovation is a novel contextual help system for the Web, and we reflect on the different methods used to evaluate it and how research insights endure attempted dissemination as a commercial product. Although the extent to which any innovation succeeds commercially depends on a number of factors like market forces, we found that our HCI innovation with user-centered origins was in a unique position to gain traction with customers and garner buy-in from investors. However, since end users were not the buyers of our product, a strong user-centered focus obfuscated other critical needs of the startup and pushed out perspectives of non-user-centered stakeholders. To make the research-to-product transition, we had to focus on adoption-centered design, the process of understanding and designing for adopters and stakeholders of the product. Our case study raises questions about how we evaluate the novelty and research contributions of HCI innovations with respect to their potential for commercial impact.
Regional citrate anticoagulation in continuous venovenous haemodiafiltration using commercial solutions.

BACKGROUND Treatment with trisodium citrate provides an effective means of regional anticoagulation during continuous renal replacement therapy (CRRT). We evaluated the efficacy, safety and cost of a regional citrate anticoagulation protocol using commercial solutions in 17 critically ill patients treated with continuous venovenous haemodiafiltration (CVVHDF). We performed a total of 22 sessions. METHODS We delivered an A.C. D-A(541(R)) solution containing 112.9 mmol/l disodium citrate (3.22%) at a median rate of 260 (190-280) ml/h via the pre-filter port of a COBE PRISMA with an AN-69 dialyser, while adjusting the rate to maintain post-filtered ionized calcium (iCa(2+)) between 0.25 and 0.4 mmol/l. Plasma iCa(2+) was maintained at >1.1 mmol/l by infusion of calcium chloride at a median rate of 1.70 (1.36-2.27) mmol/h. The dialysate was easily modified according to the acid-base status of each patient. Both replacement and dialysate solutions were delivered at 1200 ml/h. Each session was scheduled for 48 h and biological parameters were assessed every 6 h. RESULTS The mean dialyser survival was 39 +/- 11 h (median 41.5 h; range 13-48 h). We observed dialyser clotting in four cases (18%). There were no bleeding events or modifications of coagulation parameters. The citrate solution, replacement solution and dialysate were obtained as commercial products. Both the replacement and dialysate solutions contained calcium. The extra cost of this technique was 25 euro;/day as compared to anticoagulation with heparin. CONCLUSIONS We designed an efficient method of regional citrate anticoagulation for CVVHDF by using commercial solutions. The monitoring of patients was as intensive as during heparin anticoagulation for CRRT. Because of the higher cost of this method, it should be proposed only for patients with high bleeding risk.
Activation of Gibberellin Biosynthesis and Response Pathways by Low Temperature during Imbibition of Arabidopsis thaliana Seeds On-line version contains Web-only data.

Exposure of imbibed seeds to low temperature (typically 4°C) is widely used to break seed dormancy and to improve the frequency of germination. However, the mechanism by which temperature accelerates germination is largely unknown. Using DNA microarray and gas chromatography–mass spectrometry analyses, we found that a subset of gibberellin (GA) biosynthesis genes were upregulated in response to low temperature, resulting in an increase in the level of bioactive GAs and transcript abundance of GA-inducible genes in imbibed Arabidopsis thaliana seeds. Using a loss-of-function mutant, the cold-inducible GA biosynthesis gene, AtGA3ox1, was shown to play an essential role in mediating the effect of low temperature. Besides temperature, AtGA3ox1 also is positively regulated by active phytochrome and negatively regulated by GA activity. We show that both red light and GA deficiency act in addition to low temperature to elevate the level of AtGA3ox1 transcript, indicating that multiple signals are integrated by the AtGA3ox1 gene to control seed germination. When induced by low temperature, AtGA3ox1 mRNA was detectable by in situ RNA hybridization in an additional set of cell types relative to that in red light–induced seeds. Our results illustrate that the GA biosynthesis and response pathways are activated during seed imbibition at low temperature and suggest that the cellular distribution of bioactive GAs may be altered under different light and temperature conditions.
PASSALIDAE: STATE OF LARVAL TAXONOMY WITH DESCRIPTION OF NEW WORLD SPECIES

Larvae of 12 New World Species of Passalidae are described and 7 species redescribed, bringing the total number of species described to 134 worldwide. A key is provided for all New World genera. Basic setal pattern differences differentiate New World Passalini from Proculini, with the latter tribe showing 2 basic groups of genera. Some exceptions to these basic patterns suggest possible nomenclatural changes.
A new difference expansion transform in triplets for reversible data hiding

Difference expansion (DE) has been widely used for reversible data hiding. In this paper, a novel transform which embeds two bits of information in a triplet of coefficients is presented. This transform can be applied in spatial or frequency domains and induces minimum distortion to the initial data or coefficients. The proposed method outperforms all similar DE methods using triplets in terms of computational cost, visual quality and bitrate.