Miracle-dz/UniFAR-FTUs huggingface dataset:
Neutral fitness landscapes in signalling networks

Biological and technological systems process information by means of cascades of signals. Be they interacting genes, spiking neurons or electronic transistors, information travels across these systems, producing, for each set of external conditions, an appropriate response. In technology, circuits performing specific complex tasks are designed by humans. In biology, however, design has to be ruled out, confronting us with the question of how these systems could have arisen by accumulation of small changes. The key factor is the genotype–phenotype map. With the exception of RNA folding, not much is known about the exact nature of this mapping. Here, we show that structure of the genotype–phenotype map of simple feed-forward circuits is very close to the ones found in RNA; they have a large degree of neutrality, by which a circuit can be completely rewired keeping its input–output function intact, and there is a relatively small neighbourhood of a given circuit containing almost all the phenotypes.
Proportional analysis of pig kidney arterial segments: differences from the human kidney.

PURPOSE To present a systematic study and a proportional analysis of the arterial segments of the pig kidney. MATERIALS AND METHODS Sixty-one three-dimensional endocasts of the arterial segments of pig kidneys were studied. Each segment was injected with a resin of a different color. Cavalieri's principle was used to calculate the volume of each renal segment, and these results were compared with the results from the point-counting planimetry method used on photographs of pig-kidney surfaces. RESULTS Two to five renal segments were observed. Division into two segments, a cranial and a caudal, was the most common (42.62%). The renal volume ranged from 101 to 173 cm(3) (mean 130.85 cm(3)). The cranial segment was present in 39 of the 57 casts (68.42%). It presented the greatest median value of proportional area (50.00%) and also the greatest maximum value of proportional area, accounting for as much as 74.04% of the total kidney area. The ventral segment, which was found in 20 of the 57 casts (35.09%), presented the lowest median value of proportional area (13.87%) and showed the most variation in area (coefficient of variation 72.89%). There was no significant statistical difference between the segmental areas as evaluated by Cavalieri's principle and by the point-counting planimetry method. CONCLUSIONS The distribution and size of the renal-arterial segments in pigs are not similar to those of the human kidneys. Therefore, this information must be taken into account by practitioners of urologic training or ablation using pigs as the animal model, as the structure of the porcine arterial segments cannot be transposed to humans.
Reflections on a Reflective Cycle: A Tale of Knowledge Development in Design Practice

This paper explores the way design rules are developed and enacted. Literature on design stresses that scientific knowledge should be used as input for constructing a coherent repertoire of design rules. In line with the reflective cycle, these rules have to be tested and refined during their application in organizational praxis. However, in this paper we argue that do not particularly consider this process as linear and unproblematic. More specifically, our research reveals major impediments to the establishment of allegedly tested and grounded design rules. The paper illustrates this by drawing on a longitudinal case study on the evolution of a piece of design knowledge. As a result, the study provides an understanding of the specific conditions and elements that may inhibit or encourage the development and enactment of technological rules at the interface of science and design. It adds support to the importance of considering the (1) cognitive and (2) socio-political process in which design rules gain ‘good currency’ in design praxis and sets an agenda for further studying the development and enactment process of design knowledge.
Intellectual disability and other neuropsychiatric outcomes in high-risk children of mothers with schizophrenia, bipolar disorder and unipolar major depression.

BACKGROUND Recent evidence points to partially shared genetics of neuropsychiatric disorders. AIMS We examined risk of intellectual disability and other neuropsychiatric outcomes in 3174 children of mothers with schizophrenia, bipolar disorder or unipolar major depression compared with 3129 children of unaffected mothers. METHOD We used record linkage across Western Australian population-based registers. The contribution of obstetric factors to risk of intellectual disability was assessed. RESULTS Children were at significantly increased risk of intellectual disability with odds ratios (ORs) of 3.2 (95% CI 1.8-5.7), 3.1 (95% CI 1.9-4.9) and 2.9 (95% CI 1.8-4.7) in the maternal schizophrenia, bipolar disorder and unipolar depression groups respectively. Multivariate analysis suggests familial and obstetric factors may contribute independently to the risk. Although summated labour/delivery complications (OR = 1.4, 95% CI 1.0-2.0) just failed to reach significance, neonatal encephalopathy (OR = 7.7, 95% CI 3.0-20.2) and fetal distress (OR = 1.8, 95% CI 1.1-2.7) were independent significant predictors. Rates of rare syndromes in children of mothers with mental disorder were well above population rates. Risk of pervasive developmental disorders, including autism, was significantly elevated for children of mothers with bipolar disorder. Risk of epilepsy was doubled for children of mothers with unipolar depression. CONCLUSIONS Our findings provide epidemiological support for clustering of neuropsychiatric disorders. Further larger epidemiological studies are warranted.
Awareness of the Food and Drug Administration's Bad Ad Program and Education Regarding Pharmaceutical Advertising: A National Survey of Prescribers in Ambulatory Care Settings

The U.S. Food and Drug Administration's Bad Ad program educates health care professionals about false or misleading advertising and marketing and provides a pathway to report suspect materials. To assess familiarity with this program and the extent of training about pharmaceutical marketing, a sample of 2,008 health care professionals, weighted to be nationally representative, responded to an online survey. Approximately equal numbers of primary care physicians, specialists, physician assistants, and nurse practitioners answered questions concerning Bad Ad program awareness and its usefulness, as well as their likelihood of reporting false or misleading advertising, confidence in identifying such advertising, and training about pharmaceutical marketing. Results showed that fewer than a quarter reported any awareness of the Bad Ad program. Nonetheless, a substantial percentage (43%) thought it seemed useful and 50% reported being at least somewhat likely to report false or misleading advertising in the future. Nurse practitioners and physician assistants expressed more openness to the program and reported receiving more training about pharmaceutical marketing. Bad Ad program awareness is low, but opportunity exists to solicit assistance from health care professionals and to help health care professionals recognize false and misleading advertising. Nurse practitioners and physician assistants are perhaps the most likely contributors to the program.
Observation of η_{c}(1S) and η_{c}(2S) decays to K^{+}K^{-}π^{+}π^{-}π^{0} in two-photon interactions The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters

We study the processes γγ → K 0 S K ± π ∓ and γγ → K + K − π + π − π 0 using a data sample of 519.2 fb − 1 recorded by the B A B AR detector at the PEP-II asymmetric-energy e + e − collider at center-of-mass energies near the Υ ( nS ) ( n = 2 , 3 , 4) resonances. We observe the η c (1 S ), χ c 0 (1 P ) and η c (2 S ) resonances produced in two-photon interactions and decaying to K + K − π + π − π 0 , with signiﬁcances of 18 . 1, 5 . 4 and 5 . 3 standard deviations (including systematic errors), respectively, and report 4 . 0 σ evidence of the χ c 2 (1 P ) decay to this ﬁnal state. We measure the η c (2 S ) mass and width in K 0 S K ± π ∓ decays, and obtain the values m ( η c (2 S )) = 3638 . 5 ± 1 . 5 ± 0 . 8 MeV /c 2 and Γ( η c (2 S )) = 13 . 4 ± 4 . 6 ± 3 . 2 MeV, where the ﬁrst uncertainty is statistical and the second is systematic. We measure the two-photon width times branching fraction for the reported resonance signals, and search for the χ c 2 (2 P ) resonance, but no signiﬁcant signal is observed.
Relaxed Phylogenetics and Dating with Confidence

In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of “relaxed phylogenetics. ” Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.
Myelodysplastic syndromes in South America: A multinational study of 1080 patients

There are previously reported data describing differences between Asian and European patients with Myelodysplastic Syndromes (MDS), few direct comparisons based on cancer registration characteristics or using cohorts to validate scoring systems. This is the first study from South‐America, which attempts to describe demographic, clinical features, and outcome of MDS patients. We retrospectively analyzed 1,080 patients with de novo MDS from Argentina (635), Brazil (345), and Chile (100). Chilean patients were younger (P = 0.001) with female preponderance (P = 0.071). Brazilian series showed a higher predominance of RARS subtype regarding FAB and WHO classifications (P < 0.001). Hemoglobin levels were significantly lower in Brazilian and Chilean series (P < 0.001), and Chilean series also showed a lower platelet count (P = 0.028), with no differences concerning the neutrophil count, % BM blast, and the distribution of cytogenetic risk groups (P > 0.05). Chilean series depicted a lower overall survival (OS; 35 months vs. 56 months‐Argentine; 55 months‐Brazil, P = 0.030), which was consistent with a higher predominance of the high‐risk group according both to the IPSS and IPSS‐R (P = 0.046 and P < 0.001). The IPSS‐R system and its variables showed a good reproducibility to predict clinical outcome for the whole South‐American population. Epidemiological and clinical characteristics, distribution among prognostic subgroups, the OS, and the access to disease modifying therapies were more similar between Argentinean and Brazilian compared with Chilean MDS series. This will need further analysis in a larger group of patients. Descriptive and comparative studies are necessary to establish epidemiological features useful for public health attitudes to generate suitable therapeutic schemes. Am. J. Hematol. 90:851–858, 2015. © 2015 Wiley Periodicals, Inc.
Re‐evaluation of MIS 3 glaciation using cosmogenic radionuclide and single grain luminescence ages, Kanas Valley, Chinese Altai

Previous investigations observed a period of major glacial advances in Central Asia during marine oxygen isotope stage (MIS) 3 (57–29 ka), out of phase with global ice volume records. We have re‐examined the Kanas moraine complex in the Altai Mountains of Central Asia, where an MIS 3 glaciation had been previously inferred. New and consistent cosmogenic exposure and single‐grain luminescence ages indicate that the Kanas complex was formed during MIS 2 (29–12 ka), which brings its timing in line with the global ice volume record. We also identified a lateral moraine from a more extensive ice extent that dates to late MIS 5/MIS 4. To place our results in a wider contextual framework, we review the chronologies of another 26 proposed major MIS 3 glacial advances in Central Asia. For most of these sites, we find that the chronological data do not provide an unequivocal case for MIS 3 glaciation.
Infections by Human Coronavirus-NL in Hospitalized Children

Background: A new human coronavirus (HCoV), HCoV-NL, was recently reported for Dutch patients with acute respiratory tract infections (ARTI). Little information is available on the incidence, clinical manifestations and epidemiologic features of HCoV-NL infections. Methods: We performed a prospective study of symptomatic (case subjects with ARTI) and asymptomatic (control subjects undergoing elective surgery) children, ≤3 years of age, hospitalized in Canada during 2 winter seasons (2001–2003), to look at the prevalence of respiratory viruses. Reverse transcription-PCR assays were used to retrospectively detect HCoV-NL and to correlate its presence with clinical symptoms. Results: HCoV-NL was detected in nasopharyngeal aspirates from 3.0% of young children (12 of 396 children) hospitalized for treatment of ARTI (case subjects), compared with 1.7% of asymptomatic control subjects (3 of 177 children) (P = 0.6). Nine (75.0%) of the symptomatic children had mixed viral infections. The mean age and mean duration of hospitalization of case subjects were 10.1 months and 4.9 days, respectively. Final diagnoses consisted of bronchiolitis or bronchitis (9 of 12 cases), pneumonitis (1 of 12 cases) and upper respiratory tract infections (2 of 12 cases), although 2 of 3 subjects with single HCoV-NL infections had upper respiratory tract infections only. Sequence analysis of the 1a and spike genes revealed that multiple HCoV-NL strains circulated in the same geographical area in each of the 2 winter seasons. Variability was more pronounced for the spike gene, with 2 clusters of strains. Conclusions: HCoV-NL was not a major respiratory pathogen in Canada during our study, as shown by its low detection rate in hospitalized children with ARTI, coupled with the high frequency of additional pathogens and its occasional detection in healthy children.
Consensus of discrete-time multi-agent systems with nonlinear local rules and time-varying delays

In a multi-agent system (MAS), the agents are often considered to be autonomous entities, such as robots or software programs, each under the influence of a local rule, representing its interaction with other agents. Over the past few years, most research in the study of discrete-time MAS's concentrates on linear local rules. However, local interactions between agents are more likely to be governed by nonlinear rules with time-varying delays. This paper investigates the consensus of discrete-time MAS's with nonlinear local rules and time-varying delays. Based on a representative model, we obtain some basic criteria for the consensus of such MAS's. These results cover several existing results as special cases. Moreover, the above criteria are applied to the consensus of the classical Vicsek model with time-varying delays. Simulation results are presented to validate the obtained criteria.
OSNAP: Faster Numerical Linear Algebra Algorithms via Sparser Subspace Embeddings

An oblivious subspace embedding (OSE) given some parameters ε, d is a distribution D over matrices Π ∈ R<sup>m×n</sup> such that for any linear subspace W ⊆ R<sup>n</sup> with dim(W) = d, P<sub>Π~D</sub>(∀x ∈ W ||Πx||<sub>2</sub> ∈ (1 ± ε)||x||<sub>2</sub>) > 2/3. We show that a certain class of distributions, Oblivious Sparse Norm-Approximating Projections (OSNAPs), provides OSE's with m = O(d<sup>1+γ</sup>/ε<sup>2</sup>), and where every matrix Π in the support of the OSE has only s = O<sub>γ</sub>(1/ε) non-zero entries per column, for γ > 0 any desired constant. Plugging OSNAPs into known algorithms for approximate least squares regression, ℓ<sub>p</sub> regression, low rank approximation, and approximating leverage scores implies faster algorithms for all these problems. Our main result is essentially a Bai-Yin type theorem in random matrix theory and is likely to be of independent interest: we show that for any fixed U ∈ R<sup>n×d</sup> with orthonormal columns and random sparse Π, all singular values of ΠU lie in [1 - ε, 1 + ε] with good probability. This can be seen as a generalization of the sparse Johnson-Lindenstrauss lemma, which was concerned with d = 1. Our methods also recover a slightly sharper version of a main result of [Clarkson-Woodruff, STOC 2013], with a much simpler proof. That is, we show that OSNAPs give an OSE with m = O(d<sup>2</sup>/ε<sup>2</sup>), s = 1.
Gene Expression Pro ling of Metastatic and Nonmetastatic Colorectal Cancer Cell Lines

cDNA microarrays were used to compare the gene expression pattern of a nonmetastatic colorectal cancer cell line (SW480) with its metastatic derivative (SW620). Co-hybridization of  uorescently labeled cDNA generated from SW480 (Cy3) and SW620 (Cy5) total RNA to microarrays containing 4000 human cDNA clones revealed differential expression of 129 genes involved in the regulation of transcription, cell-cycle control and division, cell signaling, cell adhesion, and cell metabolism. The results of this microarray analysis corresponded to previously reported gene expression pro ling experiments with SW480 and SW620 using SAGE. Predictably, the metastatic cell line SW620 exhibited underexpression of genes involved in cell adhesion and overexpression of genes involved in transcription and translation compared with its nonmetastatic counterpart SW480. Finally, by applying a novel bioinformatics approach to the gene expression data, a number of genes underexpressed in SW620 compared with SW480 were demonstrated to map to chromosomal band 17q21-23, a region that may be associated with loss of heterozygosity during the metastatic progression of colorectal cancer.
Google Search Intensity and Stock Returns in Frontier Markets: Evidence from the Vietnamese Market

The study investigates investor attention's impact on stock trading by modeling the relationship between Google search intensity and stock return with stocks listed in frontier markets in Vietnam from October 2016 to October 2021. The study has three findings. First, the study confirms the price pressure hypothesis and attention theory that Google search intensity positively affects stock returns. Second, this study indicates that the impact of Google search intensity on stock price is short. The positive effect is within the week of searching and reverses the following week, although the reverse force is not strong. Third, the relationship is more robust post than pre-COVID-19, suggesting that after a shock, more new individual investors enter the market, the impact of GSVI on stock return is stronger.
Prospective versus retrospective measurement of change in health status: a community based study in Geneva, Switzerland.

STUDY OBJECTIVES: To compare prospective and retrospective measurements of change in health status. DESIGN: Health status was measured using a French language version of the short form 36 (SF-36) health survey on two occasions one year apart--in 1992 and 1993. Differences in SF-36 scores measured prospectively were compared with the patients' single item retrospective evaluation of change in health (transition item). SETTING: This was a community based study among members of two health insurance plans in Geneva, Switzerland. PARTICIPANTS: Altogether 831 young adults (mean age 30 years at baseline). MAIN RESULTS: Health status remained stable on average during the study period. The retrospective rating correlated well with changes in health measured prospectively: those who said in 1993 that their current health was "much worse" than in 1992 experienced an average decrease of 1.06 SD on the eight SF-36 scales, while those who said that their health was "much better" recorded an average improvement of 0.43 SD. The associations between prospective and retrospective assessments of change were approximately linear for all scales but physical functioning. The transition item also discriminated between time periods: transition reported for 1991-92 did not correlate with changes recorded for 1992-93. Relative validity analyses indicated that the transition item was better suited to capture changes in general health than changes in purely physical or mental aspects of health. CONCLUSIONS: The concordance between retrospective and prospective measures of change in health suggests that both are sensitive, to some extent, to true changes in health status. Using both types of assessment may improve the reliability of measurements of change.
Evaluation of SMAP, SMOS, and AMSR2 soil moisture retrievals against observations from two networks on the Tibetan Plateau

Two soil moisture and temperature monitoring networks were established in the Tibetan Plateau (TP) during recent years. One is located in a semihumid area (Naqu) of central TP and consists of 56 soil moisture and temperature measurement (SMTM) stations, the other is located in a semiarid area (Pali) of southern TP and consists of 21 SMTM stations. In this study, the station data are used to evaluate soil moisture retrievals from three microwave satellites, i.e., the Soil Moisture Active Passive (SMAP) of NASA, the Soil Moisture and Ocean Salinity (SMOS) of European Space Agency, and the Advanced Microwave Scanning Radiometer 2 (AMSR2) of Japan Aerospace Exploration Agency. It is found that the SMAP retrievals tend to underestimate soil moisture in the two TP networks, mainly due to the negative biases in the effective soil temperature that is derived from a climate model. However, the SMAP product well captures the amplitude and temporal variation of the soil moisture. The SMOS product performs well in Naqu network with acceptable error metrics but fails to capture the temporal variation of soil moisture in Pali network. The AMSR2 products evidently exaggerate the temporal variation of soil moisture in Naqu network but dampen it in Pali network, suggesting its retrieval algorithm needs further improvements for the TP.