Miracle-dz/UniFAR-FTUs huggingface dataset:
Production of auto-anti-idiotypic antibody during the normal immune response to TNP-ficoll. II. Hapten-reversible inhibition of anti-TNP plaque-forming cells by immune serum as an assay for auto-anti-idiotypic antibody

Sera taken from AKR/J mice 7 d after the intravenous injection of 2,4,6-trinitrophenyl-lys-Ficoll (TNP-F) caused a specific inhibition of anti- trinitrophenol (TNP) plaque-forming cells (PFC) in vitro. This inhibition was reversed by the incorporation of 10(-8)-10(-7) M 2,4,6-trinitrophenyl- ε-amino-n-caproic acid (TNP-EACA) into the agar during the PFC assay. The factor responsible for the hapten-reversible PFC inhibition was removed from serum by passage through an anti-immunoglobulin column or through a 2,4,-dinitrophenyl-human-serum-albumin-bromoacetylcellulose plus anti-TNP- antibody column, but not by DNP-HSA-BAC alone. It was concluded that this immunoglobulin-like substance, lacking anti-TNP activity but reacting with anti-TNP antibody of AKR/J origin, was most likely an auto-anti-idiotypie antibody that had been produced during the normal course of the response of AKR/J mice to TNP-F. Pools of anti-idiotypic-antibody-containing antisera inhibited anti-TNP plaque formation to varying degrees when tested on d-4 PFC from different mice of the same inbred strain, suggesting a variability in idiotype expression. 4 d after transfer of immune (7 d after 10 μg TNP-F, administered intravenously) AKR/J spleen cells plus 10 μg TNP-F into syngeneic mice, the number of PFC detectable in the recipients' spleens could be markedly augmented by the inclusion of TNP-EACA in the agar during the PFC assay. Incubation of spleen cells containing such hapten-augmentable PFC with TNP- EACA yielded a factor in the supernate that caused a specific, in vitro, hapten-reversible inhibition of anti-TNP PFC. Studies with immunoadsorbents indicated that this PFC-inhibiting factor was antigenically immunoglobulin- like, lacked anti-TNP-antibody activity, but reacted with anti-TNP antibody of AKR/J origin. The results are consistent with the view that this PFC inhibitor is auto-anti-idiotypic antibody that is involved in the normal regulation of the immune response. It is proposed that hapten-reversible inhibition of plaque formation can be employed as an assay for anti-idiotypic antibody and the conditions for such an assay are described. It is further proposed that the detection of hapten-augmentable PFC suggests the presence of auto-anti-idiotypic antibody.
Acute Hepatitis Due to Shen-Min: A Herbal Product Derived From Polygonum multiflorum

Shen-Min is a herbal product sold as a supplement for women to enhance hair growth. It is widely available across Asia, Europe, and the United States and sold without prescription as a hair nutritional supplement. We describe a case of acute liver injury in a 28-year-old white woman who developed symptomatic hepatitis 8 weeks after starting Shen-Min. All other potential causes of acute hepatitis including viral, hypoxic/ischemic, metabolic, and autoimmune etiologies were excluded. The liver injury slowly resolved over 3 weeks after discontinuing the herbal product. Although the mechanism of Shen-Min hepatotoxicity is unknown, we suspect an idiosyncratic reaction because the patient developed a fine maculopapular rash, mild eosinophilia, and did not overdose. Shen-Min is a Chinese herbal product with a mixture of several plants and vitamins including Polygonum multiflorum, a root that has been previously associated with hepatotoxicity. Nonetheless to our knowledge this is the first reported case of herbal-induced hepatotoxicity in a patient taking Shen-Min per se. Clinicians taking care of patients with acute hepatitis of unclear etiology should be aware that the consumption of Shen-Min, a hair supplement widely available in the United States and Western countries might cause acute hepatitis.
Report of the 13th Vancomycin-Resistant Staphylococcus aureus Isolate from the United States

ABSTRACT Vancomycin-resistant Staphylococcus aureus (VRSA), an important multidrug-resistant organism of public health concern, has been infrequently identified in the United States since 2002. All previous VRSA isolates belonged to clonal complex 5, a lineage associated primarily with health care. This report describes the most recent (13th) U.S. VRSA isolate, the first to be community associated.
PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms*

The PROTEOFORMER pipeline feeds ribosome profiling-driven information into an MS/MS search space. The pipeline has been greatly expanded and updated since its first publication. These novelties are presented and validated with matching MS/MS data, leading to the endorsement of a set of new proteoforms on MS/MS level and to a collection of general considerations for the ribosome profiling-based proteogenomics community. Graphical Abstract Highlights PROTEOFORMER adds ribosome profiling information to MS/MS search spaces. The PROTEOFORMER pipeline is greatly expanded and updated since its first publication. New features are demonstrated with matching ribosome profiling and MS/MS data. Experiments lead to MS/MS-proven proteoforms and general proteogenomic notices. PROTEOFORMER is a pipeline that enables the automated processing of data derived from ribosome profiling (RIBO-seq, i.e. the sequencing of ribosome-protected mRNA fragments). As such, genome-wide ribosome occupancies lead to the delineation of data-specific translation product candidates and these can improve the mass spectrometry-based identification. Since its first publication, different upgrades, new features and extensions have been added to the PROTEOFORMER pipeline. Some of the most important upgrades include P-site offset calculation during mapping, comprehensive data pre-exploration, the introduction of two alternative proteoform calling strategies and extended pipeline output features. These novelties are illustrated by analyzing ribosome profiling data of human HCT116 and Jurkat data. The different proteoform calling strategies are used alongside one another and in the end combined together with reference sequences from UniProt. Matching mass spectrometry data are searched against this extended search space with MaxQuant. Overall, besides annotated proteoforms, this pipeline leads to the identification and validation of different categories of new proteoforms, including translation products of up- and downstream open reading frames, 5′ and 3′ extended and truncated proteoforms, single amino acid variants, splice variants and translation products of so-called noncoding regions. Further, proof-of-concept is reported for the improvement of spectrum matching by including Prosit, a deep neural network strategy that adds extra fragmentation spectrum intensity features to the analysis. In the light of ribosome profiling-driven proteogenomics, it is shown that this allows validating the spectrum matches of newly identified proteoforms with elevated stringency. These updates and novel conclusions provide new insights and lessons for the ribosome profiling-based proteogenomic research field. More practical information on the pipeline, raw code, the user manual (README) and explanations on the different modes of availability can be found at the GitHub repository of PROTEOFORMER: https://github.com/Biobix/proteoformer.
The Concept of Word in Young Children as a Function of Level of Cognitive Development.

The developmental nature of the reflective concept of "word" in young children (ages 4.0 to 1.8) was investigated, and the degree to which these developmental aspects of metalinguistic awareness correspond to levels of cognitive development as described by Piaget (preoperational, transitional, and cognitive operational) was studied. Results showed that a conscious awareness of the structural and significatory aspects of words follow what Papandropoulou and Sinclair have termed "a long and slow elaboration" characterized by an initial inexact notion equating "a word" with the totality of an utterance to the conceptualization of a word in terms of component letters. It is suggested that the printed word, by virtue of being a stable, ilobjectified" referent, plays a significant role in turning the child's conscious attention to language as an opaque object of study. Implications for instruction are offered. In order to deal with the requirements of most programs of beginning reading instruction, children must be able to step back and treat language as an object that can be studied in its own right; they must be "metalinguistically aware" (e.g., Mattingly, 1972; Gleitman & Rozin, 1973). Challenged by the need to identify necessary prerequisites for undertaking formal reading instruction, researchers have sought to determine young children's ability to deal analytically with language. If "cracking the code" is an integral part of the acquisition of reading, then a necessary prerequisite for the neophyte reader is to grasp the understanding that there in fact exists a code that needs to be cracked. This "conceptual" understanding of the nature and purpose of reading is not a given for many young children (Downing, 1976; Vernon, 1971); they may not share their teachers' understanding of what "reading" is (Reid, 1966) much less what terms such as word, sentence, and sound refer to (Francis, 1973). For example, a first grade teacher's request to "Tell me which word doesn't The authors wish to express their appreciation to Pamela Lemer for her assistance in the collection of the data, and to the two anonymous reviewers for their helpful comments on the original draft of this article.
On the need for Embodied and Dis-Embodied Cognition

This essay proposes and defends a pluralistic theory of conceptual embodiment. Our concepts are represented in at least two ways: (i) through sensorimotor simulations of our interactions with objects and events and (ii) through sensorimotor simulations of natural language processing. Linguistic representations are “dis-embodied” in the sense that they are dynamic and multimodal but, in contrast to other forms of embodied cognition, do not inherit semantic content from this embodiment. The capacity to store information in the associations and inferential relationships among linguistic representations extends our cognitive reach and provides an explanation of our ability to abstract and generalize. This theory is supported by a number of empirical considerations, including the large body of evidence from cognitive neuroscience and neuropsychology supporting a multiple semantic code explanation of imageability effects.
AEGIS: THE NATURE OF THE HOST GALAXIES OF LOW-IONIZATION OUTFLOWS AT z < 0.6

We report on a signal-to-noise (S/N) limited search for low-ionization gas outflows in the spectra of the 0.11 < z < 0.54 objects in the Extended Groth Strip portion of the DEEP2 survey. Doppler shifts from the host galaxy redshifts are systematically searched for in the Na i λ 5890, 96 doublet (Na i D). Although the spectral resolution and S/N limit us to study the interstellar gas kinematics from fitting a single doublet component to each observed Na i D profile, the typical outflow often seen in local luminous-infrared galaxies (LIRGs) should be detected at ≳ 6σ in absorption equivalent width down to the survey limiting S/N (∼5 pixel−1) in the continuum around Na i D. The detection rate of LIRG-like outflow clearly shows an increasing trend with star-forming activity and infrared luminosity. However, by virtue of not selecting our sample on star formation, we also find a majority of outflows in galaxies on the red sequence in the rest-frame (U − B, MB) color–magnitude diagram. Most of these red-sequence galaxies hosting outflows are of early-type morphology and show the sign of recent star formation in their UV–optical colors; some show enhanced Balmer Hβ absorption lines indicative of poststarburst as well as high dust extinction. These findings demonstrate that outflows outlive starbursts and suggest that galactic-scale outflows play a role in quenching star formation in the host galaxies on their way to the red sequence. The fate of relic winds, as well as the observational constraints on gaseous feedback models, may be studied in galaxies during their poststarburst phase. We also note the presence of inflow candidates in red, early-type galaxies, some with signs of active galactic nuclei/LINERs but little evidence for star formation.
Genetic Algorithm application for the optimization of solid state devices using a novel modeling technique

A new method for developing a realistic physical model of any type of solid state device is presented. Application to model advanced multi-junction solar cells; Thermo-photovoltaics; sensors; as well as other novel solid state devices are introduced in this presentation. The primary goal of multijunction solar cell design is to maximize the output power for a given solar spectrum. The construction of multijunction cells places the individual junction layers in series, thereby limiting the overall output current to that of the junction layer producing the lowest current. The solution to optimizing a multijunction design involves both the design of individual junction layers which produce an optimum output power and the design of a series-stacked configuration of these junction layers which yields the highest possible overall output current. This paper demonstrates the use of genetic algorithm in a two-part process to refine a given multijunction solar cell design for near-optimal output power for a desired light spectrum. This approach can similarly be utilized to optimize the parameters of any Solid state device to yield any desired performance.
Family income and children’s outcomes: evidence for the UK

This thesis explores inequalities in educational attainment by family background, focusing on three specific aspects of this important issue. University participation is one outcome which displays large gaps by family background. I examine the effect of debt aversion on university participation and find firstly, that young people from all family backgrounds who are debt averse are less likely to attend university when they finish school, and secondly, that the size of this effect does not differ substantially by family background. Thus whilst debt aversion poses a barrier to entry into university, it doesn’t explain the gap in participation rates by family background. In fact, these gaps open up much earlier and are already apparent when the children are still very young. The second empirical chapter uses data at ages 5 and 7 to explore this further, and shows that family income itself seems to have a direct impact on children’s cognitive test scores at these ages, with other important influential factors including the stability of the child’s environment, the presence of the natural father, and parental behaviours such as taking the child to the library regularly. As well as highlighting the importance of these and other factors, this chapter makes a methodological contribution by introducing an augmented random effects model which helps address issues of endogeneity and a lack of within-variation in key variables that have faced similar studies in the past. Finally, children’s test scores demonstrate substantial stochastic variation, with the implication that the development trajectories of groups divided according to ability and family background may demonstrate regression to the mean effects. Dealing with this statistical phenomenon using various methods in order to isolate the substantive effects of family background confirms that bright children from poorer families do drop behind their peers, providing justification for a continued policy focus on this group. The existence of inequalities in educational outcomes by family background also has implications for social mobility, which further highlights the importance of investing in the cognitive development of young children from disadvantaged backgrounds.
Management of Intra-Aortic Balloon Pumps

Intra-aortic balloon pumps (IABPs) continue to be the most widely used cardiac support devices with an annual estimate of 200 000 IABPs placed worldwide. IABPs enhance myocardial function by maximizing oxygen supply and minimizing oxygen demand. The use of IABPs is not without risk, with major vascular injury, ischemia, and infection being the most common complications, especially in high-risk patients. While recent studies have questioned the use of IABPs in patients with cardiogenic shock secondary to myocardial infarction, these studies have limitations making it difficult to formulate definitive conclusions. This review will focus on the mechanisms of counterpulsation, the management of IABPs and the evidence supporting this ventricular support therapy.
The influence of the disease and treatment on the life of patients with Parkinson’s disease

Objective: As the Dutch society is ageing the prevalence of Parkinson’s disease also will rise in the Netherlands. There is still no cure for Parkinson’s disease and known treatments are focusing on suppressing the symptoms and improving the Health Related Quality of Life of the patient. The objective is to research the influence of the Parkinson’s disease, symptoms and the treatment on the life of the patient from his or hers perspective. The focus will lie on the influence of the symptoms, the positive and negative treatment outcomes and treatment characteristic’s on the patient’s life. Methods: Parkinson’s disease patients were recruited from the area of Enschede and a total of seventeen were included in the research. Quantitative data is gathered with the use of (modified) HRQoL questionnaires and qualitative data with the use of semi-structured interviews. Results: The quantitative results showed that relative the most respondents reported problems on the domains: cognitions, communication and bodily discomfort. Absolutely most problems were found with daily tasks, communication, and mobility. The qualitative results from the interviews showed that the greatest influence on their life were problems on the domains cognitions and communication. Problems caused by physical symptoms or disabilities had a smaller influence in contrast with what the quantitative data would suppose. The respondents diluted the influence of emotions, depression in particular, during the interviews. Fear of the future and disease progression was of influence of a substantial part of the respondents. This resulted in postponing adjustment of the treatment to the disease progression. Conclusion: In daily life PD symptoms cause disabilities or problems performing normal tasks. However the respondents focus more on abilities as disabilities. The greatest influence on the life of the patient was the influence of the disease symptoms and adverse effects on the dimensions cognitions and communication and the fear of progression of the symptoms.
Orohanditest: A new method for orofacial damage assessment

Background: Currently, orofacial sequelae are recognized as very influential on the quality-of-life for a victim of orofacial damage. Therefore, correct forensic assessment for indenisation purposes is mandatory. However, orofacial damage is frequently reduced to organic components, which results in a forensic assessment process, which are inadequate. This study aims to improve the orofacial damage assessment through the development of an auxiliary tool, the orohanditest. Materials and Methods: A preliminary inventory was constructed, using relevant bibliographic elements and retrospective study of forensic examinations reports concerning orofacial trauma. This inventory was then utilized in the assessment of 265 orofacial trauma victims for validation. Validity was studied by analyzing the internal construct validity (exploring factorial validity and assessing internal consistency) and the external construct validity (assessing convergent validity and discriminant validity). The level of significance was defined as P < 0.05. Results: The final inventory (orohanditest) was comprised of the three components of body (8 items), functions (10 items) and situations (24 items), which were found to be statistically reliable and valid for assessment. The final score (orofacial damage coefficient) reflects the orofacial damage severity. Conclusion: Orohanditest provides a reliable, precise, and complete orofacial damage description and quantification. Therefore, this method can be useful as an auxiliary tool in the orofacial damage assessment process.
Autophagy Modulates Cell Mineralization on Fluorapatite-Modified Scaffolds

As a major intracellular degradation and recycling machinery, autophagy plays an important role in maintaining cellular homeostasis and remodeling during normal development. Our previous study showed that fluorapatite (FA) crystal-coated electrospun polycaprolactone (PCL) was capable of inducing differentiation and mineralization of human dental pulp stem cells. However, how autophagy changes and whether autophagy plays a vital role during these processes is still unknown. In this study, we seeded STEMPRO human adipose-derived stem cells (ASCs) on both PCL+FA and PCL scaffolds to investigate the osteogenic inductive ability of FA crystals and we observed the autophagy changes of these cells. Scanning electron microscopy and fluorescence microscopy images, along with DNA quantitation, showed that both PCL+FA and PCL scaffolds could sustain ASC growth but only the PCL+FA scaffold could sustain cell mineralization. This was confirmed by alkaline phosphatase activity and Alizarin red and Von Kossa staining results. The autophagy RT2 Profiler polymerase chain reaction array analysis showed many autophagy-related genes changes during ASC differentiation. Western blot analysis indicated that several autophagy-related proteins fluctuated during the procedure. Among them, the microtubule-associated protein 1 light chain 3 (LC3)-II protein changes of the ASCs grown on the 2- or 3-dimensional environments at 6 h, 12 h, 1 d, 3 d, 7 d, 14 d, and 21 d reached a peak value at day 7 during osteogenesis. At earlier stages (from day 0 to day 3), the addition of autophagy inhibitors (3-mathyladenine, bafilomycin A1, and NH4Cl) attenuated the expression of osteogenic related markers (osteopontin, alkaline phosphatase activity, Alizarin red, and Von Kossa) compared with the control group. All data indicated that autophagy played an important role in ASC differentiation on the PCL+FA scaffold. Inhibition of autophagy before day 3 strongly inhibited osteogenic differentiation and mineralization of ASCs in the 3-dimensional model. This observation further elucidates the mechanism of autophagy in mesenchymal stem cell osteogenic differentiation.
Random Geometric Graphs and the Initialization Problem for Wireless Networks

The initialization problem, also known as naming, assigns one unique identifier (ranging from $1$ to $n$) to a set of $n$ indistinguishable nodes (stations or processors) in a given wireless network $\mathcal{N}$. $\mathcal{N}$ is composed of $n$ nodes randomly deployed within a square (resp. a cube) $X$. We assume the time to be slotted and $\mathcal{N}$ to be synchronous; two nodes are able to communicate if they are within a distance at most $r$ of each other ($r$ is the transmitting/receiving range). Moreover, if two or more neighbors of a processor $u$ transmit concurrently at the same round, $u$ does not receive either messages. After the analysis of various critical transmitting/sensing ranges for connectivity and coverage of randomly deployed sensor networks, we design sub-linear randomized initialization and gossiping algorithms with running time $\BO\l(n^{1/2} \log{(n)}^{1/2}\r)$ and $\BO\l(n^{1/3} \log{(n)}^{2/3}\r)$) in the two-dimensional and the three-dimensional cases, respectively. Next, we propose energy-efficient initialization and gossiping algorithms running in time $\BO\l(n^{3/4} \log{(n)}^{1/4}\r)$, with no station being awake for more than $\BO\l(n^{1/4}\log{(n)}^{3/4}\r)$ rounds.