Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient and Accurate Lp-Norm Multiple Kernel Learning

Learning linear combinations of multiple kernels is an appealing strategy when the right choice of features is unknown. Previous approaches to multiple kernel learning (MKL) promote sparse kernel combinations to support interpretability. Unfortunately, l1-norm MKL is hardly observed to outperform trivial baselines in practical applications. To allow for robust kernel mixtures, we generalize MKL to arbitrary lp-norms. We devise new insights on the connection between several existing MKL formulations and develop two efficient interleaved optimization strategies for arbitrary p > 1. Empirically, we demonstrate that the interleaved optimization strategies are much faster compared to the traditionally used wrapper approaches. Finally, we apply lp-norm MKL to real-world problems from computational biology, showing that non-sparse MKL achieves accuracies that go beyond the state-of-the-art.
A new species of cellular slime mold from southern Portugal based on morphology, ITS and SSU sequences

Sampling soils to look for dictyostelids in southern Portugal we found an isolate that has a morphology that differed from any previously described species of the group. We sequenced the internally transcribed spacer (ITS) and small subunit (SSU) genes of the nuclear ribosomal RNA and found that both sequences are distinct from all previously described sequences. Phylogenetic analyses place the new species in dictyostelid Group 3 (Rhizostelids) together with D. potamoides, with which it shares 65.8% identity for ITS and 96.6% for SSU. In this paper we describe a new species of cellular slime mold, Dictyostelium ibericum, based on morphological and molecular characters. It is a small species with polar granules in its spores.
Can solar variability explain global warming since 1970

[1] The magnitude of the Sun's influence on climate has been a subject of intense debate. Estimates of this magnitude are generally based on assumptions regarding the forcing due to solar irradiance variations and climate modeling. This approach suffers from uncertainties that are difficult to estimate. Such uncertainties are introduced because the employed models may not include important but complex processes or mechanisms or may treat these in too simplified a manner. Here we take a more empirical approach. We employ time series of the most relevant solar quantities, the total and UV irradiance between 1856 and 1999 and the cosmic rays flux between 1868 and 1999. The time series are constructed using direct measurements wherever possible and reconstructions based on models and proxies at earlier times. These time series are compared with the climate record for the period 1856 to 1970. The solar records are scaled such that statistically the solar contribution to climate is as large as possible in this period. Under this assumption we repeat the comparison but now including the period 1970–1999. This comparison shows without requiring any recourse to modeling that since roughly 1970 the solar influence on climate (through the channels considered here) cannot have been dominant. In particular, the Sun cannot have contributed more than 30% to the steep temperature increase that has taken place since then, irrespective of which of the three considered channels is the dominant one determining Sun-climate interactions: tropospheric heating caused by changes in total solar irradiance, stratospheric chemistry influenced by changes in the solar UV spectrum, or cloud coverage affected by the cosmic ray flux.
BJSM reviews: A to Z of nutritional supplements: dietary supplements, sports nutrition foods and ergogenic aids for health and performance—Part 18

Part 18 extends the general amino acids overview in Part 2, by reviewing specifically glutamine and glutamate, and the tripeptide antioxidant, glutathione. Glutamine supplementation has been well studied in both clinical and exercise situations, particularly in terms of its effects on immune function. Sports drinks containing glutamine as a free amino acid or part of a dipeptide are widely available but the low levels recommended are unlikely to help improve immune or muscle function. The first product of glutamine metabolism, catalysed by the enzyme glutaminase, is the excitatory neurotransmitter glutamate. The latter has sometimes been used for supplementation. This may seem rather surprising, since its appearance in plasma at a high concentration correlates neurotoxicity and sometimes with clinical problems. Glutathione, for which glutamine is a precursor via glutamate, is a powerful antioxidant and, in its reduced form, is a good marker of antioxidant capacity, while an increase in its oxidised form is a good marker of oxidative stress. ### P Newsholme and M Krause Glutathione (γ-glutamyl-cysteinyl-glycine; GSH) is the predominant low molecular weight thiol (0.5–10 mmol/l) in mammalian cells. Most GSH (85–90%) is cytosolic, with the remainder located in organelles (including mitochondria, nuclear matrix and peroxisomes). 1 This tripeptide is a key antioxidant within cells, critical to regulating the reactive oxygen species (ROS) concentration.2 Reduced glutathione (GSH) may be used to remove damaging ROS such as H2O2 and convert it to harmless H2O, generating oxidised glutathione (GSSG) via glutathione peroxidase (figure 1). Disulphide formation and gluathionylation are reversible forms of protein covalent modification dependent on glutathione and can provide mechanisms for regulation of metabolic, signalling and transcriptional processes,3 including skeletal muscle adaptation to exercise and training.4 The cellular redox state is crucial for molecular signalling, and glutathione is a key regulator/sensor for redox status; thus strategies aiming at …
Parallel overlap assembly for the construction of computational DNA libraries.

Algorithms for computing with DNA currently require the construction of pools of molecules in which each distinct molecule represents a different starting point for the calculation. We have begun building such pools using the technique of parallel overlap assembly that is already used for the generation of diversity in biologically useful combinatorial search techniques such as gene shuffling. Unlike these applications, a pool in a molecular computer must be complete, containing all possible strands, and ordered, having minimal contamination from incorrectly assembled DNA. We present an experiment in which parallel overlap assembly is used to construct a computational pool and an experiment in which this pool is used to solve the NP-complete maximal-clique problem.
National Context and Atypical Employment

This article takes a macro-approach, examining country-level determinants of three types of atypical employment (fixed-term, part-time and self-employment) in 30 developed countries. Support is found for three hypotheses: atypical work arrangements are more prevalent (1) when there is a strong entrepreneurial culture, (2) when there are legal constraints on firms’ ability to hire and fire workers and (3) when economic constraints force workers to accept atypical employment. The article also qualitatively examines three countries’ legislative, judicial and economic histories with respect to atypical work, contrasting the three histories with the quantitative analysis.
Characterization of the Interactions between PDZ Domains of the Protein-tyrosine Phosphatase PTPL1 and the Carboxyl-terminal Tail of Fas*

The intracellular protein-tyrosine phosphatase PTPL1 has five PDZ domains and one of them, PDZ 2, has previously been shown to interact with the C-terminal tail of Fas, a member of the tumor necrosis factor receptor family. Using a peptide binding assay, we show that not only PDZ 2 but also PDZ 4 of PTPL1 interacts with high affinity with peptides derived from the C terminus of Fas. The five most C-terminal amino acid residues of Fas influence the affinity of the interaction. Whereas the glutamine and isoleucine residues in the 4th and 5th positions from the C terminus affect the interaction in a negative and positive manner, respectively, the three C-terminal amino acid residues (SLV) are necessary and sufficient for a high affinity interaction to occur. Both the carboxyl group and side chain of the valine residue at the C terminus of Fas are essential, and the leucine and serine residues in the 2nd and 3rd positions, respectively, from the C terminus are important for the interactions with PDZ 2 and PDZ 4 of PTPL1.
The effect of exercise on serum and salivary cortisol in male children.

The purpose of this study was to examine serum and salivary cortisol responses to cycling exercise in male children, 10.6 +/- 0.2 yr (mean +/- SE). Each child performed a graded exercise test on a cycle ergometer to determine VO2max. On a separate day, a 30-min bout of exercise at 70% of VO2max was performed. Blood, obtained from a venous catheter, and saliva samples were collected at rest, at 15 and 30 min of exercise, and 15 min post-exercise. The mean serum cortisol level at 15 min (7.94 +/- 1.43 micrograms.dl-1) and 30 min (8.72 +/- 1.77 micrograms.dl-1) of exercise and at 15 min post-exercise (8.21 +/- 1.59 micrograms.dl-1) were significantly greater than rest (5.54 +/- 0.86 micrograms.dl-1). The increase in salivary cortisol levels over time approached (P = 0.08), but did not reach significance. However, effect size analyses indicated that the increase in salivary cortisol at 30 min of exercise (0.64) and 15 min post-exercise (0.62) was similar to the change in serum cortisol at these same two time points (0.72 and 0.66, respectively). Serum and salivary cortisol were correlated (P < 0.05) at 15 min of exercise (r = 0.77), 30 min of exercise (r = 0.90), and 15 min post-exercise (r = 0.84), but not at rest (r = 0.46). In conclusion, 30 min of submaximal exercise at 70% of VO2max significantly increased serum cortisol level; and salivary and serum cortisol are correlated during and after exercise.
Evaluating the uses of the total score and the domain scores in the Cognitive Abilities Screening Instrument, Chinese Version (CASI C-2.0): results of confirmatory factor analysis

ABSTRACT Background: The Cognitive Abilities Screening Instrument (CASI) consists of items which are designed to measure the nine domains of cognitive ability. Its total score is used clinically to represent the overall underlying cognitive ability of the patient. This study aimed to evaluate the justification of the uses of the all-domain-total-score as an overall cognitive measure and the domain scores as measures of designated individual cognitive ability. Methods: To justify the use of total score of all the items as an overall measure of cognitive ability, a second-order confirmatory factor analysis was performed to examine whether the items in CASI contributed significantly to a common underlying construct. The uses of domain scores were also examined by inspecting the loadings of the items on their designated domains. The CASI data from 608 patients, 68 normal and 540 with Alzheimer's disease, were analyzed. Results The goodness-of-fit indices for the second-order factor model were as follows: CFI was 0.912 for WLSMV and 0.977 for WLSM; TLI and RMSEA values were 0.975 and 0.090 respectively. The loadings of the items on the common underlying construct are all salient (>0.3). The loadings of all but the long-term memory items on their respective subdomains were also salient. Conclusions: The items of the CASI C-2.0 were useful not only in profiling the correlated cognitive domain scores, but also in forming an overall measure of the underlying cognitive ability of the patients.
Cell adhesion molecule Nr‐CAM is over‐expressed in human brain tumors

Using the technique of differential display‐polymerase chain reaction (DD‐PCR), we isolated a cDNA fragment that is over‐expressed in glioblastoma multiforme tissue as compared to normal brain tissue. Sequence analysis indicated that this sequence is identical to the previously isolated human neuron‐glia‐related cell adhesion molecule hNr‐CAM. Gene‐specific RT‐PCR analysis indicated that hNr‐CAM is over‐expressed in high‐grade astrocytomas, gliomas and glioblastoma tumor tissues as compared to normal brain tissue. High levels of hNr‐CAM expression also were observed in cell lines derived from astrocytomas, gliomas and glioblastoma multiforme tumors. Low levels of hNr‐CAM expression were observed in neuroblastoma, meningiomas, melanoma, normal breast and prostate tumor tissues. Northern blot analysis showed an alternatively spliced mRNA of 1.4 kb in several tumors as compared to the 7.5 kb transcript found in normal brain tissue. Genomic Southern blot analysis of DNA from 3 brain tumor cell lines showed that over‐expression of hNr‐CAM in brain tumors was not due to gene amplification. In situ hybridization analysis indicated that 11 of the 20 human brain tumor samples studied showed hNr‐CAM over‐expression. Our results suggest that hNr‐CAM is over‐expressed in malignant brain tumors and can serve as a novel marker for brain tumor detection and perhaps therapy. Int. J. Cancer 76:451–458, 1998. © 1998 Wiley‐Liss, Inc.
Animal snoRNAs and scaRNAs with exceptional structures

The overwhelming majority of small nucleolar RNAs (snoRNAs) fall into two clearly deﬁned classes characterized by distinctive secondary structures and sequence motifs. A small group of diverse ncRNAs, however, shares the hallmarks of one or both classes of snoRNAs but diﬀers substantially from the norm in some respects. Here, we compile the available information on these exceptional cases, conduct a thorough homology search throughout the available metazoan genomes, provide improved and expanded alignments, and investigate the evolutionary histories of these ncRNA families as well as their mutual relationships.
Atmospheric Measurement Techniques A field-deployable , chemical ionization time-of-flight mass spectrometer

We constructed a new chemical ionization timeof-flight mass spectrometer (CI-TOFMS) that measures atmospheric trace gases in real time with high sensitivity. We apply the technique to the measurement of formic acid via negative-ion proton transfer, using acetate as the reagent ion. A novel high pressure interface, incorporating two RF-only quadrupoles is used to efficiently focus ions through four stages of differential pumping before analysis with a compact TOFMS. The high ion-duty cycle ( >20 %) of the TOFMS combined with the efficient production and transmission of ions in the high pressure interface results in a highly sensitive (>300 ions s−1 pptv−1 formic acid) instrument capable of measuring and saving complete mass spectra at rates faster than 10 Hz. We demonstrate the efficient transfer and detection of both bare ions and ion-molecule clusters, and characterize the instrument during field measurements aboard the R/V Atlantisas part of the CalNex campaign during the spring of 2010. The in-field short-term precision is better than 5 % at 1 pptv (pL/L), for 1-s averages. The detection limit (3 σ , 1-s averages) of the current version of the CITOFMS, as applied to the in situ detection of formic acid, is limited by the magnitude and variability in the background determination and was determined to be 4 pptv. Application of the CI-TOFMS to the detection of other inorganic and organic acids, as well as the use of different reagent ion molecules (e.g. I , CF3O, CO − 3 ) is promising, as we have demonstrated efficient transmission and detection of both bare ions and their associated ion-molecule clusters. Correspondence to: T. H. Bertram (thbertram@ucsd.edu)
Efficient algorithms for the blind recovery of images blurred by multiple filters

We address the problem of restoring an image from its noisy convolutions with two or more unknown blur functions. We extend some of the results developed for the multichannel blind deconvolution problem in one dimension. When the unknown blur functions have no common factors, we present algorithms to estimate them quickly and accurately. Once the blur functions are available, they can be used to reconstruct the unknown image. We show that, under certain conditions, the last step can be achieved by FIR filtering with a perfect reconstruction filter bank. Some results on the effects of noise on these algorithms are also presented.
Overlap of ADHD and oppositional defiant disorder DSM-IV derived criteria.

OBJECTIVE One possible reason for being controversies regarding ADHD may be related to the validity and reliability of diagnostic criteria of attention deficit hyperactivity disorder and oppositional defiant disorder. Diagnostic criteria of oppositional defiant disorder include eight symptoms. This study examines the factor structure of oppositional defiant disorder symptoms, its discriminant validity from attention deficit hyperactivity disorder, its convergent validity and internal reliability. METHODS Parents of 111 referral children and adolescents with attention deficit hyperactivity disorder completed DSM-IV referenced based attention deficit hyperactivity disorder and oppositional defiant disorder checklists. RESULTS Factor analysis indicated that the attention deficit hyperactivity disorder symptom of: "often has trouble organizing activities" and "often runs about or climbs when and where it is not appropriate" were a part of the oppositional defiant disorder component. These symptoms less often than other symptoms differentiate attention deficit hyperactivity disorder from oppositional defiant disorder. The convergent validity for oppositional defiant disorder symptoms ranged from 0.64 to 0.79. CONCLUSION The parent-rating checklist of oppositional defiant disorder symptoms properly differentiates oppositional defiant disorder from attention deficit hyperactivity disorder. However, two items of the attention deficit hyperactivity disorder were listed as symptoms of oppositional defiant disorder. If the factor loading of the items is to be confirmed in further studies, it might be necessary to revise these symptoms criterion in future editions of DSM-IV diagnostic criteria.
Teacher feedback during active learning: current practices in primary schools.

BACKGROUND Feedback is one of the most powerful tools, which teachers can use to enhance student learning. It appears difficult for teachers to give qualitatively good feedback, especially during active learning. In this context, teachers should provide facilitative feedback that is focused on the development of meta-cognition and social learning. AIMS The purpose of the present study is to contribute to the existing knowledge about feedback and to give directions to improve teacher feedback in the context of active learning. SAMPLE The participants comprised 32 teachers who practiced active learning in the domain of environmental studies in the sixth, seventh, or eighth grade of 13 Dutch primary schools. A total of 1,465 teacher-student interactions were examined. METHODS Video observations were made of active learning lessons in the domain of environmental studies. A category system was developed based on the literature and empirical data. Teacher-student interactions were assessed using this system. Results. About half of the teacher-student interactions contained feedback. This feedback was usually focused on the tasks that were being performed by the students and on the ways in which these tasks were processed. Only 5% of the feedback was explicitly related to a learning goal. In their feedback, the teachers were directing (rather than facilitating) the learning processes. CONCLUSIONS During active learning, feedback on meta-cognition and social learning is important. Feedback should be explicitly related to learning goals. In practice, these kinds of feedback appear to be scarce. Therefore, giving feedback during active learning seems to be an important topic for teachers' professional development.
Identification of a Member of the MAPKKK Family as a Potential Mediator of TGF-β Signal Transduction

The mitogen-activated protein kinase (MAPK) pathway is a conserved eukaryotic signaling module that converts receptor signals into various outputs. MAPK is activated through phosphorylation by MAPK kinase (MAPKK), which is first activated by MAPKK kinase (MAPKKK). A genetic selection based on a MAPK pathway in yeast was used to identify a mouse protein kinase (TAK1) distinct from other members of the MAPKKK family. TAK1 was shown to participate in regulation of transcription by transforming growth factor-β (TGF-β). Furthermore, kinase activity of TAK1 was stimulated in response to TGF-β and bone morphogenetic protein. These results suggest that TAK1 functions as a mediator in the signaling pathway of TGF-β superfamily members.
Bio-social origins of depression in the community

Background Social adversity may be a risk factor for depression, by increasing Cortisol secretion, which impairs serotonin (5-HT) neurotransmission. Aims To examine this causal pathway in a community setting. Method Women who were currently ICD–10 depressed (n=94), vulnerable to depression but not depressed (n=166) and non-vulnerable controls (n=177) were recruited. We assessed social adversity and vulnerability (Life Eventsand Difficulties Schedule; Self Evaluation and Social Support Scales) and psychiatric state (Schedules for Clinical Assessment in Neuropsychiatry). Salivary cortisol concentrations were measured at 09.00 and 23.00 h. Serotonin function was assessed using prolactin responses to dexfenfluramine. Results Cortisol concentrations were not increased in the depressed or vulnerable. Morning salivary and serum cortisol were reduced in depression. Evening cortisol was increased after recent life events. Life events and depression were associated with increased prolactin responses. Conclusions The hypothalamic–pituitary–adrenal axis is sensitive to social stress but does not mediate vulnerability to depression. Exaggerated 5-HT2 receptor responsiveness to stress may play a role in the evolution of depression.
T1‐ and T2‐weighted fast spin‐echo imaging of the brachial plexus and cervical spine with IDEAL water–fat separation

To compare the iterative decomposition of water and fat with echo asymmetry and least‐squares estimation (IDEAL) method with fat‐saturated T1‐weighted (T1W) and T2W fast spin‐echo (FSE) and short‐TI inversion recovery (STIR) imaging of the brachial plexus and cervical spine.
Measles virus and canine distemper virus target proteins into a TAP-independent MHC class I-restricted antigen-processing pathway.

After infection of CEM174.T2 cells [deficient for the transporter of antigen presentation (TAP)] with measles virus (MV) the nucleocapsid protein is recognized by L(d)-restricted cytotoxic T cells in a TAP-independent, chloroquine-sensitive fashion. Presentation via the TAP-independent pathway requires virus replication. During MV infection of the cell the nucleocapsid as well as the matrix protein enter the endolysosomal compartment as indicated by colocalization with the lysosomal-associated membrane protein 1 (LAMP-1). Similarly, the nucleocapsid protein of canine distemper virus (CDV) is recognized in a TAP-independent fashion. In addition, a recombinant MV expressing bacterial beta-galactosidase protein is able to introduce the recombinant antigen into the TAP-independent pathway whereas a vaccinia virus expressing beta-galactosidase is not. These data and a report about TAP-independent recognition of parainfluenza virus type 1 suggest that members of the Paramyxoviridae family regularly introduce viral proteins into the TAP-independent antigen-processing pathway.