Miracle-dz/UniFAR-FTUs huggingface dataset:
Autotrophic Stoichiometry Emerging from Optimality and Variable Co-limitation

Autotrophic organisms reveal an astounding flexibility in their elemental stoichiometry, with potentially major implications on biogeochemical cycles and ecological functioning. Notwithstanding, stoichiometric regulation and co-limitation by multiple resources in autotrophs \revt{were in the past often} described by heuristic formulations. In this study, we present a mechanistic model of autotroph growth, which features two major improvements over the existing schemes. First, we introduce the concept of metabolic network independence that defines the degree of phase-locking between accessory machines. Network independence is in particular suggested to be proportional to protein synthesis capability as quantified by variable intracellular N:C. Consequently, the degree of co-limitation becomes variable, contrasting with the dichotomous debate on the use of Liebig's law or the product rule, standing for constantly low and high co-limitation, respectively. Second, we resolve dynamic protein partitioning to light harvesting, carboxylation processes, and to an arbitrary number of nutrient acquisition machineries, as well as instantaneous activity regulation of nutrient uptake. For all regulatory processes we assume growth rate optimality, here extended by an explicit consideration of indirect feed-back effects. The combination of network independence and optimal regulation displays unprecedented skill in reproducing rich stoichiometric patterns collected from a large number of published chemostat experiments. This high skill indicates (1) that the current paradigm of fixed co-limitation is a critical short-coming of conventional models, and (2) that stoichiometric flexibility in autotrophs possibly reflects an optimality strategy. Numerical experiments furthermore show that regulatory mechanisms homogenize the effect of multiple stressors. Extended optimality alleviates the effect of the most limiting resource(s) while down-regulating machineries for the less limiting ones, which induces an ubiquitous response surface of growth rate over ambient resource levels.
WT1 peptide immunotherapy for cancer in children and young adults

Wilms tumor gene (WT1) can be overexpressed in childhood cancers. We evaluated the efficacy of WT1 vaccination for five children with solid cancer or acute leukemia. WT1 vaccine was administered to HLA‐A*2402‐positive patients with WT1‐overexpressing residual tumor despite prior conventional treatment. One patient showed complete response and one patient showed stable disease according to the Response Evaluation Criteria in Solid Tumors; the remaining three showed progressive disease. Treatment‐related adverse effects were limited to local injection site erythema. These results suggest that WT1 vaccination has therapeutic potential, but any beneficial effect may be insufficient in the presence of gross residual disease. Pediatr Blood Cancer. 2010;55:352–355. © 2010 Wiley–Liss, Inc.
SlideWorld: A multidisciplinary research project to reinvent the videoconferencing user experience

SlideWorld is a Bell Labs research project that aims to create a new immersive user experience in the situation of videoconferencing. It addresses two types of user experiences: the remote listener's immersion in the event and the speaker's augmented feedback channel from the remote listeners. Such innovation may leverage technical novelties (such as smile detection) or usage novelties (such as virtual neighbors selected in a crowd). SlideWorld is an example of a successful project that managed to innovate by smoothly integrating technical and usage novelties. To do so, a multidisciplinary team of computer scientists, ergonomists, and designers ran several rounds of design, development, and experimentation to define/refine the user experience and its actual implementation. This paper exemplifies this typical multidisciplinary work.
Hydrogen adsorption on Li metal in boron substituted graphene: ab initio approach

The characteristics of hydrogen adsorption on Li metal atoms dispersed on graphene with boron substitution were investigated for Li clustering, hydrogen bonding characteristics and open metal states of Li adatom by using density functional theory calculations. It is found that Li atoms are well dispersed on boron substituted graphene and can form the (2 × 2) pattern because clustering of Li atoms is hindered by repulsive Coulomb interaction between Li atoms. One Li adatom dispersed on the double side of graphene can absorb up to 8 hydrogen molecules corresponding to 13.2% hydrogen storage capacity. In addition, adsorption behaviors of non-hydrogen atoms such as C, B, and O2 are calculated to find whether Li atom can be remained as open metal state in boron substituted graphene.
PLPD: reliable protein localization prediction from imbalanced and overlapped datasets

Subcellular localization is one of the key functional characteristics of proteins. An automatic and efficient prediction method for the protein subcellular localization is highly required owing to the need for large-scale genome analysis. From a machine learning point of view, a dataset of protein localization has several characteristics: the dataset has too many classes (there are more than 10 localizations in a cell), it is a multi-label dataset (a protein may occur in several different subcellular locations), and it is too imbalanced (the number of proteins in each localization is remarkably different). Even though many previous works have been done for the prediction of protein subcellular localization, none of them tackles effectively these characteristics at the same time. Thus, a new computational method for protein localization is eventually needed for more reliable outcomes. To address the issue, we present a protein localization predictor based on D-SVDD (PLPD) for the prediction of protein localization, which can find the likelihood of a specific localization of a protein more easily and more correctly. Moreover, we introduce three measurements for the more precise evaluation of a protein localization predictor. As the results of various datasets which are made from the experiments of Huh et al. (2003), the proposed PLPD method represents a different approach that might play a complimentary role to the existing methods, such as Nearest Neighbor method and discriminate covariant method. Finally, after finding a good boundary for each localization using the 5184 classified proteins as training data, we predicted 138 proteins whose subcellular localizations could not be clearly observed by the experiments of Huh et al. (2003).
Appreciative Inquiry: Change at the Speed of Imagination

The Case for a New Approach to Change. Appreciative Inquiry: History, Theory, and Research. Appreciative Inquiry As a Process. Choose the Positive As the Focus of Inquiry. Inquire into Stories of Life--Giving Forces. Locate Themes That Appear in the Stories. Create Shared Images for a Preferred Future. Find Innovative Ways to Create that Preferred Future. Evaluation.
Post-weaning Exposure to High-Fat Diet Induces Kidney Lipid Accumulation and Function Impairment in Adult Rats

Aim: We investigated the kidney morphofunctional consequences of high-fat diet intake since post-weaning in adult rats. Main Methods: Male Wistar rats were divided into two groups: ND (normal diet; n = 10) and HD (high-fat diet; n = 10). The high-fat diet was introduced post-weaned and animals were followed for 8 weeks. Key Findings: HD group did not change body weight gain even though food consumption has decreased with no changes in caloric consumption. The HD group showed glucose intolerance and insulin resistance. The glomerular filtration rate (GFR) was decreased in vivo (ND: 2.8 ± 1.01; HD: 1.1 ± 0.14 ml/min) and in the isolated perfusion method (34% of decrease). Renal histological analysis showed a retraction in glomeruli and an increase in kidney lipid deposition (ND: 1.5 ± 0.17 HD: 5.9 ± 0.06%). Furthermore, the high-fat diet consumption increased the pro-inflammatory cytokines IL-6 (ND: 1,276 ± 203; HD: 1,982 ± 47 pg/mL/mg) and IL-1b (ND: 97 ± 12 HD: 133 ± 5 pg/mL/mg) without changing anti-inflammatory cytokine IL-10. Significance: Our study provides evidence that high-fat diet consumption leads to renal lipid accumulation, increases inflammatory cytokines, induces glomeruli retraction, and renal dysfunction. These damages observed in the kidney could be associated with an increased risk to advanced CKD in adulthood suggesting that reduction of high-fat ingestion during an early period of life can prevent metabolic disturbances and renal lipotoxicity.
Prenatal Nutritional Intervention Reduces Autistic-Like Behavior Rates Among Mthfr-Deficient Mice

The causes and contributing factors of autism spectrum disorders (ASD) are poorly understood. One gene associated with increased risk for ASD is methylenetetrahydrofolate-reductase (MTHFR), which encodes a key enzyme in one carbon (C1) metabolism. The MTHFR 677C > T polymorphism reduces the efficiency of methyl group production with possible adverse downstream effects on gene expression. In this study, the effects of prenatal and/or postnatal diets enriched in C1 nutrients on ASD-like behavior were evaluated in Mthfr-deficient mice. Differences in intermediate pathways between the mice with and without ASD-like behaviors were tested. The findings indicate that maternal and offspring Mthfr deficiency increased the risk for an ASD-like phenotype in the offspring. The risk of ASD-like behavior was reduced in Mthfr-deficient mice supplemented with C1 nutrients prenatally. Specifically, among offspring of Mthfr+/- dams, prenatal diet supplementation was protective against ASD-like symptomatic behavior compared to the control diet with an odds ratio of 0.18 (CI:0.035, 0.970). Changes in major C1 metabolites, such as the ratios between betaine/choline and SAM/SAH in the cerebral-cortex, were associated with ASD-like behavior. Symptomatic mice presenting ASD-like behavior showed decreased levels of GABA pathway proteins such as GAD65/67 and VGAT and altered ratios of the glutamate receptor subunits GluR1/GluR2 in males and NR2A/NR2B in females. The altered ratios, in turn, favor receptor subunits with higher sensitivity to neuronal activity. Our study suggests that MTHFR deficiency can increase the risk of ASD-like behavior in mice and that prenatal dietary intervention focused on MTHFR genotypes can reduce the risk of ASD-like behavior.
The Role of Parental Concerns in the Recognition of Sepsis in Children: A Literature Review

Background: Sepsis is a time critical disease and outcomes strongly depend on time to initiation of appropriate treatment in hospital. A range of studies have assessed sepsis recognition in hospital settings, whereas little is known about sepsis recognition in the community. The decision-making of parents in seeking medical care may substantially impact survival of children with sepsis. An improved understanding of the parental perspective in recognizing sepsis is urgently needed to inform the design of education campaigns and consideration of using parental concerns as a trigger in sepsis screening tools. Aim: To review the literature on parental concerns in the diagnosis of sepsis in children. Methods: A literature review on parental concerns in pediatric sepsis was performed accessing publications in PubMed, CINAHL and Medline published between 1990 and 2018. In addition, we compared guidelines and online institutional sepsis recognition tools and assessed whether parental concerns were used for screening. Results: Out of 188 articles reviewed, 11 met the criteria. One article was found prospectively assessing the diagnostic performance of parental concern in children evaluated for infection, indicating high positive (16.4) and negative likelihood ratio (0.23) for sepsis/meningitis in presence of parental concerns. The role of parental concern was listed as a sign assisting recognition of sepsis in four studies reporting original data, and six reviews commented on parental concern listed as a factor upon diagnosis of sepsis. When comparing selected examples of institutional sepsis pathways available online, parental concern was variably listed as a criterion to prompt evaluation for sepsis. Conclusions: Despite some guidelines emphasizing the role of parental concern in recognizing sepsis, there is a paucity of data in the field. An improved understanding of whether parental concerns adds diagnostic value to sepsis recognition at acceptable sensitivity and specificity is urgently needed. Future prospective studies should assess whether including parental concerns in sepsis screening tools benefits the assessment resulting in early diagnosis and treatment of children with sepsis.
Topic-aware sentiment prediction for Chinese ConceptNet

Sentiment dictionary is a valuable resource in sentiment analysis research. Previous works propagate sentiment values from existing high quality dictionary on semantic networks to build wide coverage dictionary efficiently. But this approach suffers from quality degradation during propagation. In this work, we propose a topic-aware propagation method on Chinese ConceptNet to ease the issue. With this approach, every terms will have different sentiment values under different topics. The experimental result shows that the generated topic-aware sentiment dictionary helps improve the performance of polarity classification for texts.
The major histocompatibility complex of rhesus monkeys. VI. Serology and genetics of Ia-like antigens.

The serology and genetics of 11 new cell surface alloantigens of rhesus monkeys are described. They are controlled by the major histocompatibility complex but are distinct from the conventional serologically defined (SD) antigens of RHL—A. The new specificities are termed “la-like” because of serological, immunocytological and other characteristics reminiscent of la-antigens of the mouse. Population and family analyses led to the postulation of two segregant series controlling eight of the 11 la-like specificities of the monkey. Strong linkage disequilibria with SD2 antigens and genetic mapping on the basis of segregation studies in recombinant Offspring in the monkey families, places at least one of the two loci in the vicinity of the SD2 locus of RHL—A, not in the region of the major MLC or LD1 locus. For this and other reasons, the new B-cell alloantigens of rhesus monkeys are not believed to be similar to or associated with the stimulator antigens of LD1. The biological function(s) of the la-like antigens of primates are as yet unknown.
Large Language Models to Generate System-Level Test Programs Targeting Non-functional Properties

System-Level Test (SLT) has been a part of the test flow for integrated circuits for over a decade and still gains importance. However, no systematic approaches exist for test program generation, especially targeting non-functional properties of the Device under Test (DUT). Currently, test engineers manually compose test suites from off-the-shelf software, approximating the end-user environment of the DUT. This is a challenging and tedious task that does not guarantee sufficient control over non-functional properties. This paper proposes Large Language Models (LLMs) to generate test programs. We take a first glance at how pre-trained LLMs perform in test program generation to optimize non-functional properties of the DUT. Therefore, we write a prompt to generate C code snippets that maximize the instructions per cycle of a super-scalar, out-of-order architecture in simulation. Additionally, we apply prompt and hyperparameter optimization to achieve the best possible results without further training.
RAPIDO Testing and Modeling of Assisted Write and Read Operations for SRAMs

Lowering the supply voltage of Static Random-Access Memories (SRAM) is key to reduce an integrated circuit power consumption, however since this badly affects the circuit performances, it might lead to various failure modes of the memory circuit. While it is known that assist techniques can help in recovering functionality, it is hard to find a detailed model of those techniques. In this work, static write- and read-assist techniques are used to lower the minimum operating voltage VMIN of a high-density 6T SRAM circuit manufactured in 40nm technology. A newly-developed spice-based method allows modeling at high computing efficiency the effects of static negative bit-line write-assist and the effects of static word-line under-drive read-assist on memory yield. Silicon results collected over a large temperature range on a die population show that 100mV static negative bit-line is enough to lower the memory supply voltage to Vddnom - 250mV safely. Despite its simplicity, the model allows to reproduce the salient features of silicon data.
Modeling and Emulation of Internet Paths

Network emulation subjects real applications and protocols to controlled network conditions. Most existing network emulators are fundamentally link emulators, not path emulators: they concentrate on faithful emulation of the transmission and queuing behavior of individual network hops in isolation, rather than a path as a whole. This presents an obstacle to constructing emulations of observed Internet paths, for which detailed parameters are difficult or impossible to obtain on a hop-by-hop basis. For many experiments, however, the experimenter's primary concern is the end-to-end behavior of paths, not the details of queues in the interior of the network. End-to-end measurements of many networks, including the Internet, are readily available and potentially provide a good data source from which to construct realistic emulations. Directly using such measurements to drive a link emulator, however, exposes a fundamental disconnect: link emulators model the capacity of resources such as link bandwidth and router queues, but when reproducing Internet paths, we generally wish to emulate the measured availability of these resources. In this paper, we identify a set of four principles for emulating entire paths. We use these principles to design and implement a path emulator. All parameters to our model can be measured or derived from end-to-end observations of the Internet. We demonstrate our emulator's ability to accurately recreate conditions observed on Internet paths.
From source model to quantum key distillation: An improved upper bound

In this paper we derive a new upper bound on the quantum key distillation capacity. This upper bound is an extension of the classical bound of Gohari and Anantharam on the source model problem. Our bound strictly improves the quantum extension of reduced intrinsic information bound of Christandl et al. Although this bound is proposed for quantum settings, it also serves as an upper bound for the special case of classical source model, and may improve the bound of Gohari and Anantharam. The problem of quantum key distillation is one in which two distant parties, Alice and Bob, and an adversary, Eve, have access to copies of quantum systems A, B, E respectively, prepared jointly according to an arbitrary state ρABE. Alice and Bob desire to distill secret key bits that are secure from Eve, using only local quantum operations and authenticated public classical communication (LOPC).
Effects of 4-weeks of asynchronous hand-rim wheelchair practice on mechanical efficiency and timing

Purpose. To investigate the consequence on gross mechanical efficiency (GE), arm frequency and sub-maximal performance, of paced and unpaced practice during asynchronous hand-rim wheelchair propulsion. Methods. Twenty-five able-bodied participants performed five, 4-min exercise bouts at 1.7 m/s, at the freely chosen frequency (FCF) and four paced arm frequencies of 60, 80, 120 and 140% FCF. GE, arm frequency and measures of sub-maximal performance were determined. Participants were assigned to an unpaced (FCF, N = 9), paced (80% FCF, N = 8) or control (CON, N = 8) no practice group. The FCF and 80% FCF groups received 4-weeks (unpaced and paced, respectively) propulsion practice (three sessions·per wk, four 4 min/trials; 33–35 W) at 1.7 m/s on a wheelchair ergometer. Following practice, the pre-testing protocol was repeated. Results. Mean GE showed a relative increase in both experimental groups (21 and 17%; FCF and 80% FCF respectively; p = 0.001) compared to no change in CON (−1.5%). The FCF arm frequency decreased in both experimental groups (p = 0.001), with larger changes evident following FCF practice. Conclusion. Four weeks of unpaced or paced practice had a beneficial effect on GE. This improvement seems to be associated with a reduction in arm frequency.
Body Ideals and Weight Bias: Does Ethnicity Make a Difference?

The current study investigates whether there are there ethnic differences between Caucasian, African American, and Hispanic women in (a) weight bias, (b) body ideals, (c) social awareness and internalization of appearance standards and (d) physical activity in relation to these constructs. Participants included 130 Caucasian, 103 African American, and 52 Hispanic undergraduate female students. Participants completed a demographic survey, the Antifat Attitudes Test, the Figure Rating Scale, the Sociocultural Attitudes toward Appearance Questionnaire, and the Multiethnic Identity Measure questionnaire. No significant ethnic group differences in weight bias emerged. Differences were found for participants' perceptions of the culturally ideal female body shape, as well as awareness and internalization. No relationship was found between physical activity and weight bias, body ideals, and appearance standards. Future researchers should use health weight classifications, in addition to ethnicity, to examine weight bias, body ideals, and physical activity.
Spectral Quadrangulation with Boundary Conformation

Existing spectral quadrangulation methods are effective only for closed surfaces, because they cannot satisfactorily handle surfaces with boundaries or feature lines that need to be respected. We propose an extension to the spectral quadrangulation approach that ensures boundary/feature conformation. Our contributions include the formulation of a set of new boundary conditions and the introduction of quasi-eigenfunctions that are solutions of a PDE with the new boundary conditions. We also develop algorithms for computing the quasi-eigenfunctions and extracting their Morse-Smale complexes to generate desired quadrangulation. We further extend the method to generating adaptive quadrangulation observing a pre-speciﬁed density function. Experiments show that our method produces better quadrilateral meshes with conforming boundaries/features and varying element size than existing methods do.
Towards automated spectroscopic tissue classification in thyroid and parathyroid surgery

In (para‐)thyroid surgery iatrogenic parathyroid injury should be prevented. To aid the surgeons’ eye, a camera system enabling parathyroid‐specific image enhancement would be useful. Hyperspectral camera technology might work, provided that the spectral signature of parathyroid tissue offers enough specific features to be reliably and automatically distinguished from surrounding tissues. As a first step to investigate this, we examined the feasibility of wide band diffuse reflectance spectroscopy (DRS) for automated spectroscopic tissue classification, using silicon (Si) and indium‐gallium‐arsenide (InGaAs) sensors.