Miracle-dz/UniFAR-FTUs huggingface dataset:
Infrared Ellipsometric Study of Hydrogen-Bonded Long-Chain Thiolates on Gold: Towards Resolving Structural Details

A set of newly synthesized aryl-substituted amides of 16-mercaptohexadecanoic acid (R = 4-OH; 3,5-di-OH) are self-assembled on Au(111) substrate. Self assembled monolayers (SAMs) formed by these molecules are studied by ellipsometry from infrared to visible spectral range. Best fit calculations based on the three-phase optical model are employed in order to determine the average tilt angle of the hydrocarbon chains. The data revealed that the SAMs reside in a crystalline-like environment as the long methylene chains predominantly exist in all-trans conformation. The calculated tilt angle of the hydrocarbon chain is decreased by approximately 12° in comparison with the one for the correspondent long-chain n-alkyl thiols. Strong hydrogen bonded networks were detected between the amide proton and the carbonyl oxygen as well as between hydroxyl groups in the end aryl substituents. The transition dipole moments of the C=O, N-H and O-H modes are oriented almost parallel to the gold surface.
Energy benefits of a configurable line size cache for embedded systems

Previous work has shown that cache line sizes impact performance differently for different desktop programs; some programs work better with small line sizes, others with larger line sizes. Typical processors come with a line size that is a compromise, working best on the average for a variety of programs. We analyze the energy impact of different line sizes, for 19 embedded system benchmarks, and we show that tuning the line size to a particular program can reduce memory access energy by 50% in some examples. Our data argues strongly for the need for embedded microprocessors to have configurable line size caches, and for embedded system designers to put effort into choosing the best line size for their programs.
Identification of Direct Targets of FUSCA3, a Key Regulator of Arabidopsis Seed Development1[C][W][OA]

A set of genes expressed during Arabidopsis embryo development are directly controlled by the transcription factor FUSCA3. FUSCA3 (FUS3) is a B3 domain transcription factor that is a member of the LEAFY COTYLEDON (LEC) group of genes. The LEC genes encode proteins that also include LEC2, a B3 domain factor related to FUS3, and LEC1, a CCAAT box-binding factor. LEC1, LEC2, and FUS3 are essential for plant embryo development. All three loss-of-function mutants in Arabidopsis (Arabidopsis thaliana) prematurely exit embryogenesis and enter seedling developmental programs. When ectopically expressed, these genes promote embryo programs in seedlings. We report on chromatin immunoprecipitation-tiling array experiments to globally map binding sites for FUS3 that, along with other published work to assess transcriptomes in response to FUS3, allow us to determine direct from indirect targets. Many transcription factors associated with embryogenesis are direct targets of FUS3, as are genes involved in the seed maturation program. FUS3 regulates genes encoding microRNAs that, in turn, control transcripts encoding transcription factors involved in developmental phase changes. Examination of direct targets of FUS3 reveals that FUS3 acts primarily or exclusively as a transcriptional activator. Regulation of microRNA-encoding genes is one mechanism by which FUS3 may repress indirect target genes. FUS3 also directly up-regulates VP1/ABI3-LIKE1 (VAL1), encoding a B3 domain protein that functions as a repressor of transcription. VAL1, along with VAL2 and VAL3, is involved in the transition from embryo to seedling development. Many genes are responsive to FUS3 and to VAL1/VAL2 but with opposite regulatory consequences. The emerging picture is one of complex cross talk and interactions among embryo transcription factors and their target genes.
Widespread plasticity in CTCF occupancy linked to DNA methylation

CTCF is a ubiquitously expressed regulator of fundamental genomic processes including transcription, intra- and interchromosomal interactions, and chromatin structure. Because of its critical role in genome function, CTCF binding patterns have long been assumed to be largely invariant across different cellular environments. Here we analyze genome-wide occupancy patterns of CTCF by ChIP-seq in 19 diverse human cell types, including normal primary cells and immortal lines. We observed highly reproducible yet surprisingly plastic genomic binding landscapes, indicative of strong cell-selective regulation of CTCF occupancy. Comparison with massively parallel bisulfite sequencing data indicates that 41% of variable CTCF binding is linked to differential DNA methylation, concentrated at two critical positions within the CTCF recognition sequence. Unexpectedly, CTCF binding patterns were markedly different in normal versus immortal cells, with the latter showing widespread disruption of CTCF binding associated with increased methylation. Strikingly, this disruption is accompanied by up-regulation of CTCF expression, with the result that both normal and immortal cells maintain the same average number of CTCF occupancy sites genome-wide. These results reveal a tight linkage between DNA methylation and the global occupancy patterns of a major sequence-specific regulatory factor.
Improved Nested Sampling and Surrogate‐Enabled Comparison With Other Marginal Likelihood Estimators

Estimating marginal likelihood is of central importance to Bayesian model selection and/or model averaging. The nested sampling method has been recently used together with the Metropolis‐Hasting (M‐H) sampling algorithm for estimating marginal likelihood. This study develops a new implementation of nested sampling by using the DiffeRential Evolution Adaptive Metropolis (DREAMzs) sampling algorithm. The two implementations of nested sampling are evaluated for four models of a synthetic groundwater flow modeling. The DREAMzs‐based nested sampling outperforms the M‐H‐based nested sampling in terms of their accuracy, convergence, efficiency, and stability, which is attributed to the fact that DREAMzs is more robust than M‐H for parameter sampling. The nested sampling method is also compared with four other methods (arithmetic mean, harmonic mean, stabilized harmonic mean, and thermodynamic integration) commonly used for estimating marginal likelihood and posterior probability of the four groundwater models. The comparative study requires hundreds of millions of model executions, which would not be possible without using surrogate models to replace the original models. Using the arithmetic mean estimator as the reference, the comparison reveals that thermodynamic integration outperforms nested sampling in terms of accuracy and stability, whereas nested sampling is more computationally efficient to reach to convergence. The harmonic mean and stabilized harmonic mean methods give the worst marginal likelihood estimation. Accurate marginal likelihood estimation is important for accurate estimation of posterior model probability and better predictive performance of Bayesian model averaging.
Neutrino masses and mixing, lightest neutralino decays and a solution to the μ problem in supersymmetry

We examine in detail the neutrino masses and mixing patterns in an extension of the minimal supersymmetric standard model with three gauge-singlet neutrinos and R-parity violation. The Majorana masses for the gauge-singlet neutrinos as well as the usual $\mu$-term for the Higgs superfields are generated at the electroweak scale through the vacuum expectation values of the singlet sneutrinos. The resulting effective mass matrix for the three light neutrinos have contributions from the seesaw mechanism involving the singlet neutrinos as well as due to the mixing with the heavy neutralinos. This model is popularly known in the literature as the "$\mu$ from $\nu$ supersymmetric standard model" ($\mu\nu$SSM). We show that even with flavour diagonal neutrino Yukawa couplings, the global data on three-flavour neutrinos can be well accounted for in this scenario, at the tree level. We also analyze the mixing in the chargino and the Higgs sector and calculate the decays of the lightest supersymmetric particle in this model. The decay branching ratios show certain correlations with the neutrino mixing angles, which can be tested at the LHC. Some other phenomenological implications of such a model have been discussed.
Evolutionary transitions in symbioses: dramatic reductions in bathymetric and geographic ranges of Zoanthidea coincide with loss of symbioses with invertebrates

Two fundamental symbiosis‐based trophic types are recognized among Zoanthidea (Cnidaria, Anthozoa): fixed carbon is either obtained directly from zooxanthellae photosymbionts or from environmental sources through feeding with the assistance of host‐invertebrate behaviour and structure. Each trophic type is characteristic of the suborders of Zoanthidea and is associated with substantial distributional asymmetries: suborder Macrocnemina are symbionts of invertebrates and have global geographic and bathymetric distributions and suborder Brachycnemina are hosts of endosymbiotic zooxanthellae and are restricted to tropical photic zones. While exposure to solar radiation could explain the bathymetric asymmetry it does not explain the geographic asymmetry, nor is it clear why evolutionary transitions to the zooxanthellae‐free state have apparently occurred within Macrocnemina but not within Brachycnemina. To better understand the transitions between symbiosis‐based trophic types of Zoanthidea, a concatenated data set of nuclear and mitochondrial nucleotide sequences were used to test hypotheses of monophyly for groups defined by morphology and symbiosis, and to reconstruct the evolutionary transitions of morphological and symbiotic characters. The results indicate that the morphological characters that define Macrocnemina are plesiomorphic and the characters that define its subordinate taxa are homoplasious. Symbioses with invertebrates have ancient and recent transitions with a general pattern of stability in host associations through evolutionary time. The reduction in distribution of Zoanthidea is independent of the evolution of zooxanthellae symbiosis and consistent with hypotheses of the benefits of invertebrate symbioses, indicating that the ability to persist in most habitats may have been lost with the termination of symbioses with invertebrates.
Major depression and stages of smoking. A longitudinal investigation.

BACKGROUND Epidemiologic studies have reported an association between major depression and smoking. This prospective study examines the role of depression in smoking progression and cessation, and the role of smoking in first-onset major depression. METHODS Data are from a 5-year longitudinal epidemiologic study of 1007 young adults. Incidence and odds ratios (ORs) are based on the prospective data. Hazards ratios are based on the combined lifetime data and estimated in Cox proportional hazards models with time-dependent covariates. RESULTS Based on the prospective data, history of major depression at baseline increased significantly the risk for progression to daily smoking (OR, 3.0; 95% confidence interval, 1.1-8.2), but did not decrease significantly smokers' rate of quitting (OR, 0.8; 95% confidence interval, 0.4-1.6). History of daily smoking at baseline increased significantly the risk for major depression (OR, 1.9; 95% confidence interval, 1.1-3.4). These estimates were reduced somewhat when history of early (ie, before age 15 years) conduct problems was controlled. Estimates based on lifetime data were consistent with these results. CONCLUSIONS The observed influences from major depression to subsequent daily smoking and smoking to major depression support the plausibility of shared etiologies. Separate causal mechanisms in each direction might also operate, including self-medication of depressed mood as a factor in smoking progression and neuropharmacologic effects of nicotine and other smoke substances on neurotransmitter systems linked to depression.
Silencing COI1 in Rice Increases Susceptibility to Chewing Insects and Impairs Inducible Defense

The jasmonic acid (JA) pathway plays a key role in plant defense responses against herbivorous insects. CORONATINE INSENSITIVE1 (COI1) is an F-box protein essential for all jasmonate responses. However, the precise defense function of COI1 in monocotyledonous plants, especially in rice (Oryza sativa L.) is largely unknown. We silenced OsCOI1 in rice plants via RNA interference (RNAi) to determine the role of OsCOI1 in rice defense against rice leaf folder (LF) Cnaphalocrocis medinalis, a chewing insect, and brown planthopper (BPH) Nilaparvata lugens, a phloem-feeding insect. In wild-type rice plants (WT), the transcripts of OsCOI1 were strongly and continuously up-regulated by LF infestation and methyl jasmonate (MeJA) treatment, but not by BPH infestation. The abundance of trypsin protease inhibitor (TrypPI), and the enzymatic activities of polyphenol oxidase (PPO) and peroxidase (POD) were enhanced in response to both LF and BPH infestation, but the activity of lipoxygenase (LOX) was only induced by LF. The RNAi lines with repressed expression of OsCOI1 showed reduced resistance against LF, but no change against BPH. Silencing OsCOI1 did not alter LF-induced LOX activity and JA content, but it led to a reduction in the TrypPI content, POD and PPO activity by 62.3%, 48.5% and 27.2%, respectively. In addition, MeJA-induced TrypPI and POD activity were reduced by 57.2% and 48.2% in OsCOI1 RNAi plants. These results suggest that OsCOI1 is an indispensable signaling component, controlling JA-regulated defense against chewing insect (LF) in rice plants, and COI1 is also required for induction of TrypPI, POD and PPO in rice defense response to LF infestation.
Influence of Cinnamon and Catnip on the Stereotypical Pacing of Oncilla Cats (Leopardus tigrinus) in Captivity

Nonhuman animals in captivity can experience environmental privation that results in their exhibiting abnormal behaviors. Environmental enrichment techniques can help improve their welfare. This study investigated the behavior of 8 zoo-housed oncilla cats (Leopardus tigrinus) in response to 2 odors (catnip and cinnamon) introduced individually into the animals' enclosures for 3 consecutive days. Proportion of scans spent engaging in stereotypical pacing were compared before, during, and after treatments. The addition of cinnamon reduced the proportion of pacing during and after enrichment (Wilcoxon: Z = 3.16, p < .001; Z = 3.16, p < .001, respectively), indicating a prolonged effect of the enrichment on the animals' behavior. Catnip appears to have elicited no significant difference in the stereotypic pacing before, during, or after the enrichment (Friedman: X2 = 2.69; p = .260). The results highlight the potential use of cinnamon as a method of environmental enrichment for small captive-housed cats.
Projected precipitation changes within the Great Lakes and Western Lake Erie Basin: a multi‐model analysis of intensity and seasonality

The Great Lakes region encompasses the largest freshwater lake network in the world and supports a diverse network of agriculture, transportation, and tourism. Recently, Lake Erie has experienced increased hypoxia events, which have been attributed to agricultural practices and changes in run‐off. Here we examine the projected changes in extreme precipitation events to address concerns regarding regional agriculture, surface run‐off, and subsequent water quality. Precipitation projections within the overall Great Lakes Basin and the Western Lake Erie Basin subregion are examined using climate model simulations of varying spatial resolutions to understand historical precipitation and projected future precipitation. We develop three model ensembles for the historical period (1980–1999) and the mid‐century (2041–2060) that cover a range of spatial resolutions and future emissions scenarios, including: (1) 12 global model members from the fifth Climate Model Intercomparison Project (CMIP5) using Representative Concentration Pathway (RCP) 8.5, (2) ten regional climate model (RCM) members from the North American Regional Climate Change Assessment Program driven by CMIP3 global models using the A2 emissions scenario, and (3) two high resolution RCM simulations (RCM4) driven by CMIP5 global models using the RCP 8.5 scenario. For the historical period, all model ensembles overestimate winter and spring precipitation, and many of the models simulate a summer drying that is not observed. At mid‐century, most of the models predict a 10–20% increase in precipitation depending on the time of year. Daily probability distribution functions from three model ensembles reveal spring seasonal increases in high precipitation event probabilities when compared to the historical period, suggesting an increase in the frequency of high intensity precipitation at mid‐century. Overall, the presence of lakes or higher spatial resolution does not ensure improved representation of historical processes, and more complex interactions between large‐scale dynamics, local feedbacks, and physical parameterizations drive the model spread.
Amphotericin B lipid complex therapy of experimental fungal infections in mice

The amphotericin B lipid complex (ABLC), which is composed of amphotericin B and the phospholipids dimyristoyl phosphatidylcholine and dimyristoyl phosphatidylglycerol, was evaluated for its acute toxicity in mice and for its efficacy in mice infected with a variety of fungal pathogens. ABLC was markedly less toxic to mice when it was administered intravenously; it had a 50% lethal dose of greater than 40 mg/kg compared with a 50% lethal dose of 3 mg/kg for Fungizone, the desoxycholate form of amphotericin B. ABLC was efficacious against systemic infections in mice caused by Candida albicans, Candida species other than C. albicans, Cryptococcus neoformans, and Histoplasma capsulatum. ABLC was also efficacious in immunocompromised animals infected with C. albicans, Aspergillus fumigatus, and H. capsulatum. Against some infections, the efficacy of ABLC was comparable to that of Fungizone, while against other infections Fungizone was two- to fourfold more effective than ABLC. Against several infections. Fungizone could not be given at therapeutic levels because of intravenous toxicity. ABLC, with its reduced toxicity, could be administered at drug levels capable of giving a therapeutic response. ABLC should be of value in the treatment of severe fungal infections in humans.
Antifungal therapy and management of complications of cryptococcosis due to Cryptococcus gattii.

BACKGROUND We describe antifungal therapy and management of complications due to Cryptococcus gattii infection in 86 Australian patients followed for at least 12 months. METHODS Patient data from culture-confirmed cases (2000-2007) were recorded at diagnosis, 6 weeks, 6 months, and 12 months. Clinical, laboratory, and treatment variables associated with raised intracranial pressure (ICP) and immune reconstitution inflammatory syndrome (IRIS) were determined. RESULTS Seven of 10 patients with lung infection received amphotericin B (AMB) induction therapy (6 with 5-flucytosine [5-FC] for a median of 2 weeks); median duration of therapy including azole eradication therapy was 41 weeks, with a complete/partial clinical response in 78%. For neurologic disease, 88% of patients received AMB, 78% with 5-FC, for a median of 6 weeks. The median total course was 18 months. Nine patients receiving fluconazole induction therapy were reinduced with AMB plus 5-FC for clinical failure. Raised ICP (31 patients) was associated with initial abnormal neurology, and neurologic sequelae and/or death at 12 months (both P = .02); cerebrospinal fluid drains/shunts were placed in 58% of patients and in 64% of 22 patients with hydrocephalus. IRIS developed 2-12 months after starting antifungals in 8 patients, who presented with new/enlarging brain lesions. Risk factors included female sex, brain involvement at presentation, and higher median CD4 counts (all P < .05); corticosteroids reduced cryptococcoma-associated edema. CONCLUSIONS Induction AMB plus 5-FC is indicated for C. gattii neurologic cryptococcosis (6 weeks) and when localized to lung (2 weeks). Shunting was often required to control raised ICP. IRIS presents with cerebral manifestations.
Expression and phylogeny of claudins in vertebrate primordia

Claudins, the major transmembrane proteins of tight junctions, are members of the tetraspanin superfamily of proteins that mediate cellular adhesion and migration. Their functional importance is demonstrated by mutations in claudin genes that eliminate tight junctions in myelin and the testis, abolish Mg2+ resorption in the kidney, and cause autosomal recessive deafness. Here we report that two paralogs among 15 claudin genes in the zebrafish, Danio rerio, are expressed in the otic and lateral-line placodes at their earliest stages of development. Related claudins in amphibians and mammals are expressed in a similar manner in vertebrate primordia such as sensory placodes, branchial arches, and limb buds. We also show that the claudin gene family may have expanded along the chordate stem lineage from urochordates to gnathostomes, in parallel with the elaboration of vertebrate characters. We propose that tight junctions not only form barriers in mature epithelia, but also participate in vertebrate morphogenesis.
Face recognition under camouflage and adverse illumination

This paper presents a method for face identification under adverse conditions by combining regular, frontal face images with facial strain maps using score-level fusion. Strain maps are generated by calculating the central difference method of the optical flow field obtained from each subject's face during the open mouth expression. Subjects were recorded with and without camouflage under three lighting conditions: normal lighting, low lighting, and strong shadow. Experimental results demonstrate that strain maps are a useful supplemental biométrie in all three adverse conditions, especially in the camouflage condition, where a 30% increase in rank 1 recognition is observed over a baseline PCA-based algorithm.
Microstructure Variations in the Soft‐Hard Tissue Junction of the Human Anterior Cruciate Ligament

The role of the sub‐bundles in the anterior cruciate ligament (ACL) has been defined, such that the anterior‐medial bundle directly resists anterior tibial translation while the posterior lateral bundle is involved in rotational stability. With regards to this biomechanical function, much of the previous work on bundle‐specific morphology has been carried out on the macroscale, with much less attention given to the micro‐to‐ultrastructural scalar levels. This is especially true of the enthesis and its microstructure, a biomechanically significant region that has been largely neglected in the published literature dealing with ACL sub‐bundle anatomy. In this study, the human ACL tibial enthesis was investigated at multiple scalar levels using differential interference contrast and scanning electron microscopies with the aim of determining whether the sub‐bundle ligament structure, and its known macroscale function, is consistent with its micro‐architecture at the ligament–bone junction. The investigation found that different ligament insertion morphologies exist between the two bundles, where the AM bundle has more intense interdigitation with the bone matrix than that of the PL bundle. The results suggest that such structure–function relationships, especially across scalar‐levels, provide new insight into the significance of the sub‐bundle anatomy of the ACL. Anat Rec, 300:1547–1559, 2017. © 2017 Wiley Periodicals, Inc.