Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning to Reason: End-to-End Module Networks for Visual Question Answering

Natural language questions are inherently compositional, and many are most easily answered by reasoning about their decomposition into modular sub-problems. For example, to answer “is there an equal number of balls and boxes? ” we can look for balls, look for boxes, count them, and compare the results. The recently proposed Neural Module Network (NMN) architecture [3, 2] implements this approach to question answering by parsing questions into linguistic substructures and assembling question-specific deep networks from smaller modules that each solve one subtask. However, existing NMN implementations rely on brittle off-the-shelf parsers, and are restricted to the module configurations proposed by these parsers rather than learning them from data. In this paper, we propose End-to-End Module Networks (N2NMNs), which learn to reason by directly predicting instance-specific network layouts without the aid of a parser. Our model learns to generate network structures (by imitating expert demonstrations) while simultaneously learning network parameters (using the downstream task loss). Experimental results on the new CLEVR dataset targeted at compositional question answering show that N2NMNs achieve an error reduction of nearly 50% relative to state-of-theart attentional approaches, while discovering interpretable network architectures specialized for each question.
Positive Affectivity and Lifestyle in Adulthood: Do You Do What You Feel?

There is much evidence for the adaptive value of positive affect. Empirical work examining different facets of positive affect and their consequences for psychological adaptation remains sparse, however. This study (young, middle-aged, and older adults; N = 293) investigated the links between two dimensions of positive affect (positive involvement and pleasant affect) and two lifestyles (hedonic and growth related), each indicated by general value orientations, self-reported everyday activities, and activity aspirations. Structural equation models showed that pleasant affect and positive involvement constitute distinct dimensions evincing different age trends and relating differentially to hedonic and growth-related lifestyles. Specifically, pleasant affect, but not positive involvement, was related to a hedonic lifestyle, whereas positive involvement, and not pleasant affect, was associated with a growth-related lifestyle. These findings underline the importance of considering two dimensions of positive affect—pleasant feelings and positive involvement—separately when studying the link between affect and lifestyle.
Nucleophosmin integrates within the nucleolus via multi-modal interactions with proteins displaying R-rich linear motifs and rRNA

The nucleolus is a membrane-less organelle formed through liquid-liquid phase separation of its components from the surrounding nucleoplasm. Here, we show that nucleophosmin (NPM1) integrates within the nucleolus via a multi-modal mechanism involving multivalent interactions with proteins containing arginine-rich linear motifs (R-motifs) and ribosomal RNA (rRNA). Importantly, these R-motifs are found in canonical nucleolar localization signals. Based on a novel combination of biophysical approaches, we propose a model for the molecular organization within liquid-like droplets formed by the N-terminal domain of NPM1 and R-motif peptides, thus providing insights into the structural organization of the nucleolus. We identify multivalency of acidic tracts and folded nucleic acid binding domains, mediated by N-terminal domain oligomerization, as structural features required for phase separation of NPM1 with other nucleolar components in vitro and for localization within mammalian nucleoli. We propose that one mechanism of nucleolar localization involves phase separation of proteins within the nucleolus. DOI: http://dx.doi. org/10.7554/eLife.13571. 001
Seeing and Hearing Meaning: ERP and fMRI Evidence of Word versus Picture Integration into a Sentence Context

Understanding language always occurs within a situational context and, therefore, often implies combining streams of information from different domains and modalities. One such combination is that of spoken language and visual information, which are perceived together in a variety of ways during everyday communication. Here we investigate whether and how words and pictures differ in terms of their neural correlates when they are integrated into a previously built-up sentence context. This is assessed in two experiments looking at the time course (measuring event-related potentials, ERPs) and the locus (using functional magnetic resonance imaging, fMRI) of this integration process. We manipulated the ease of semantic integration of word and/or picture to a previous sentence context to increase the semantic load of processing. In the ERP study, an increased semantic load led to an N400 effect which was similar for pictures and words in terms of latency and amplitude. In the fMRI study, we found overlapping activations to both picture and word integration in the left inferior frontal cortex. Specific activations for the integration of a word were observed in the left superior temporal cortex. We conclude that despite obvious differences in representational format, semantic information coming from pictures and words is integrated into a sentence context in similar ways in the brain. This study adds to the growing insight that the language system incorporates (semantic) information coming from linguistic and extralinguistic domains with the same neural time course and by recruitment of overlapping brain areas.
Molecular Phylogeny and Predicted 3D Structure of Plant beta-D-N-Acetylhexosaminidase

beta-D-N-Acetylhexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of β-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. We constructed phylogenetic tree of β-hexosaminidases to analyze the evolutionary history and predicted functions of plant hexosaminidases. Phylogenetic analysis reveals the complex history of evolution of plant β-hexosaminidase that can be described by gene duplication events. The 3D structure of tomato β-hexosaminidase (β-Hex-Sl) was predicted by homology modeling using 1now as a template. Structural conformity studies of the best fit model showed that more than 98% of the residues lie inside the favoured and allowed regions where only 0.9% lie in the unfavourable region. Predicted 3D structure contains 531 amino acids residues with glycosyl hydrolase20b domain-I and glycosyl hydrolase20 superfamily domain-II including the (β/α)8 barrel in the central part. The α and β contents of the modeled structure were found to be 33.3% and 12.2%, respectively. Eleven amino acids were found to be involved in ligand-binding site; Asp(330) and Glu(331) could play important roles in enzyme-catalyzed reactions. The predicted model provides a structural framework that can act as a guide to develop a hypothesis for β-Hex-Sl mutagenesis experiments for exploring the functions of this class of enzymes in plant kingdom.
Lower Mitochondrial Energy Production of the Thigh Muscles in Patients With Low‐Normal Ankle‐Brachial Index

Background Lower muscle mitochondrial energy production may contribute to impaired walking endurance in patients with peripheral arterial disease. A borderline ankle‐brachial index (ABI) of 0.91 to 1.10 is associated with poorer walking endurance compared with higher ABI. We hypothesized that in the absence of peripheral arterial disease, lower ABI is associated with lower mitochondrial energy production. Methods and Results We examined 363 men and women participating in the Baltimore Longitudinal Study of Aging with an ABI between 0.90 and 1.40. Muscle mitochondrial energy production was assessed by post‐exercise phosphocreatine recovery rate constant (kPCr) measured by phosphorus magnetic resonance spectroscopy of the left thigh. A lower post‐exercise phosphocreatine recovery rate constant reflects decreased mitochondria energy production.The mean age of the participants was 71±12 years. A total of 18.4% had diabetes mellitus and 4% were current and 40% were former smokers. Compared with participants with an ABI of 1.11 to 1.40, those with an ABI of 0.90 to 1.10 had significantly lower post‐exercise phosphocreatine recovery rate constant (19.3 versus 20.8 ms−1, P=0.015). This difference remained significant after adjusting for age, sex, race, smoking status, diabetes mellitus, body mass index, and cholesterol levels (P=0.028). Similarly, post‐exercise phosphocreatine recovery rate constant was linearly associated with ABI as a continuous variable, both in the ABI ranges of 0.90 to 1.40 (standardized coefficient=0.15, P=0.003) and 1.1 to 1.4 (standardized coefficient=0.12, P=0.0405). Conclusions An ABI of 0.90 to 1.10 is associated with lower mitochondrial energy production compared with an ABI of 1.11 to 1.40. These data demonstrate adverse associations of lower ABI values with impaired mitochondrial activity even within the range of a clinically accepted definition of a normal ABI. Further study is needed to determine whether interventions in persons with ABIs of 0.90 to 1.10 can prevent subsequent functional decline.
Populasi Serangga Penyerbuk Kelapa Sawit Elaeidobius kamerunicus Faust dan Pengaruhnya terhadap Nilai Fruit Set pada Tanah Berliat, Berpasir dan Gambut di Kalimantan Tengah, Indonesia

ABSTRACT Population of soil palm weevil pollinator Elaeidobius kamerunicus FAUST and its impact on fruit set value at clay, sandy and peat soil types in central Kalimantan, di Indonesia Oil palm weevil pollinator Elaeidobius kamerunicus Faust plays an important role in the increasing oil palm fruit set value. Along with the development of oil palm, fruit set problems occurred in recent decades in some parts of Indonesia. An experiment was carried out on a seven years old oil palm plantation located at Selangkun Estate, Kotawaringin Barat, Central Kalimantan, Indonesia to find out the influence of population E. kamerunicus on pollination efficiency at clay, sandy and peat soil types. Relative to other soil types, a high weevil population on male (50,811 weevils/ha ; 72 weevils/spikelet) and female (219 weevils) inflorescences had been recorded at clay soil. Fruit set value on clay soil 58.9% and significantly different with sandy soil of 49.8% and peat soil of 46.4%. Population E. kamerunicus per ha influenced fruit set value at clay, sandy and peat soil types. Number of E. kamerunicus visited female inflorescences did not influenced fruit set value at clay, sandy and peat soil types. Keywords: Clay soil, Elaeidobius kamerunicus, fruit set, peat soil, population, sandy soil ABSTRAK Serangga penyerbuk kelapa sawit Elaeidobius kamerunicus FAUST berperan penting dalam peningkatan nilai fruit set kelapa sawit. Seiring dengan perkembangan kelapa sawit, adanya permasalahan nilai fruit set telah terjadi dalam beberapa kurun waktu di beberapa wilayah Indonesia. Penelitian dilakukan di perkebunan kelapa sawit yang telah berumur tujuh tahun, berlokasi di Selangkung, Kotawaringin Barat, Kalimantan Tengah, Indonesia dan bertujuan untuk mengetahui pengaruh populasi E. Kamerunicus terhadap efisiensi penyerbukan pada tipe tanah liat, pasir dan gambut. Berdasarkan tipe tanah dilaporkan bahwa tingginya populasi kumbang pada bunga jantan yaitu (50.811 kumbang/ha; 72 kumbang/spikelet) dan bunga betina yang sedang mekar (219 kumbang) pada tipe tanah berliat. Adapun, nilai fruit set pada tanah liat sebesar 58,9% dan berbeda nyata dibandingkan dengan tanah berpasir (49,8%) dan gambut (46,4%). Populasi E. kamerunicus per ha berpengaruh terhadap nilai fruit set pada tipe tanah liat, pasir dan gambut. Namun, jumlah E. kamerunicus yang mengunjungi bunga betina yang sedang mekar tidak berpengaruh terhadap nilai fruit set pada tipe tanah liat, pasir dan gambut. Kata Kunci : Elaeidobius kamerunicus, Fruit set , Populasi, Tanah Gambut, Tanah liat, Tanah Pasir
Optical Genome Mapping Reveals Genomic Alterations upon Gene Editing in hiPSCs: Implications for Neural Tissue Differentiation and Brain Organoid Research

Genome editing, notably CRISPR (cluster regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9), has revolutionized genetic engineering allowing for precise targeted modifications. This technique’s combination with human induced pluripotent stem cells (hiPSCs) is a particularly valuable tool in cerebral organoid (CO) research. In this study, CRISPR/Cas9-generated fluorescently labeled hiPSCs exhibited no significant morphological or growth rate differences compared with unedited controls. However, genomic aberrations during gene editing necessitate efficient genome integrity assessment methods. Optical genome mapping, a high-resolution genome-wide technique, revealed genomic alterations, including chromosomal copy number gain and losses affecting numerous genes. Despite these genomic alterations, hiPSCs retain their pluripotency and capacity to generate COs without major phenotypic changes but one edited cell line showed potential neuroectodermal differentiation impairment. Thus, this study highlights optical genome mapping in assessing genome integrity in CRISPR/Cas9-edited hiPSCs emphasizing the need for comprehensive integration of genomic and morphological analysis to ensure the robustness of hiPSC-based models in cerebral organoid research.
Hepatitis C virus genotypes in liver transplant recipients: impact on posttransplant recurrence, infections, response to interferon-alpha therapy and outcome.

BACKGROUND End-stage liver disease due to hepatitis C virus (HCV) is the most common indication for liver transplantation in U.S. veterans. We investigated the influence of HCV genotypes on the incidence and timing of recurrent HCV hepatitis, survival, infectious morbidity, and response to interferon-alpha therapy in this unique patient population. METHODS HCV genotype was determined by direct sequencing of the NS5 region of HCV with type-specific primers. RESULTS Genotype 1a (66%, 32/47) was the predominant genotype. Type 1b was found in 25% (12/47) of patients and type 2b was found in 9% (4/47). Histopathologically recurrent HCV hepatitis developed in 53% (25/47) of the patients after transplantation. This group included 45% (14/31) of the patients with type 1a, 67% (8/12) of the patients with type 1b, and 25% (1/4) of the patients with type 2b (P>0.5). The time to recurrence and the severity of HCV recurrence as defined by aminotransferase levels or Knodell scores were not different among the three genotypes. There was a trend toward a higher incidence of major infections in patients with type 1b (75%) versus type 1a (48%) and type 2b (50%) (P=0.11). The response to interferon-a therapy did not differ significantly among the genotypes. Mortality at 5 years was 16% (5/31) in patients with genotype 1a, 42% (5/12) in patients with genotype 1b, and 50% (2/4) in patients with genotype 2b (P=0.06). CONCLUSIONS The incidence, time to recurrence, and response to interferon-alpha therapy did not differ between the various genotypes in our liver transplant recipients. However, there was a trend toward higher infectious morbidity and overall mortality in patients with genotype 1b after transplantation.
Alterations in the rheological flow profile in conduit femoral artery during rhythmic thigh muscle contractions in humans.

The present study examined the rheological blood velocity profile in the conduit femoral artery during rhythmic muscle contractions at different muscle forces. Eight healthy volunteers performed one-legged, dynamic knee-extensor exercise at work rates of 5, 10, 20, 30, and 40 W at 60 contractions per minute. The time and space-averaged, amplitude-weighted mean (V(mean)) and maximum (V(max)) blood flow velocities in the common femoral artery were measured during the cardiosystolic phase (CSP) and cardiodiastolic phase (CDP) by the Doppler ultrasound technique. The V(max)/V(mean) ratio was used as a flow profile index, in which a ratio of approximately 1 indicates a "flat velocity flow profile" and a ratio significantly >1 indicates a "parabolic velocity flow profile. " At rest, the V(max)/V(mean) ratio was approximately 1.3 and approximately 1.8 during the CSP and CDP, respectively. The V(max)/V(mean) ratio was higher (p < 0.01) during the CDP than during the CSP, both at rest and at all work rates. The V(max)/V(mean) ratio during the CSP was higher (p < 0.01) at 30 and 40 W compared to at rest. The V(max)/V(mean) ratio during the CDP was lower (p < 0.05) at 5 and 10 W compared to at rest. There was a positive linear correlation between blood flow and incremental work rates during both the CSP and CDP, respectively. Thus under resting conditions, the findings indicate a "steeper" parabolic velocity profile during the CDP than during the CSP. The velocity profile during the CDP furthermore shifts to being less "steep" during rhythmic muscle contractions at lower intensities, but to being reelevated and normalized as at rest during higher intensities. The "steepness" of the parabolic velocity profile observed during the CSP at rest increased during muscle contraction at higher intensities. In conclusion, the blood velocity in the common femoral artery is parabolic both at rest and during exercise for both the CSP and CDP, indicating the persistence of laminar flow. The occurrence of any temporary slight disturbance or turbulence in the flow at the sight of measurement in the common femoral artery does consequently not induce a persisting "disturbed" and fully flat "plug-like" velocity profile. Instead, the "steepness" of the parabolic velocity profile is only slightly modified, whereby blood flow is not impaired. Thus the blood velocity profile, besides being influenced by the muscle contraction-relaxation induced mechanical "impedance," seems also to be modulated by the cardiac- and blood pressure-phases, consequently influencing the exercise blood flow response.
Effects of different dietary protein sources on expression of genes related to protein metabolism in growing rats

Protein metabolism is known to be affected by dietary proteins, but the fundamental mechanisms that underlie the changes in protein metabolism are unclear. The aim of the present study was to test the effects of feeding growing rats with balanced diets containing soya protein isolate, zein and casein as the sole protein source on the expression of genes related to protein metabolism responses in skeletal muscle. The results showed that feeding a zein protein diet to the growing rats induced changes in protein anabolic and catabolic metabolism in their gastrocnemius muscles when compared with those fed either the reference protein casein diet or the soya protein isolate diet. The zein protein diet increased not only the mRNA levels and phosphorylation of mammalian target of rapamycin (mTOR), but also the mRNA expression of muscle atrophy F-box (MAFbx)/atrogin-1 and muscle ring finger 1 (MuRF1), as well as the forkhead box-O (FoxO) transcription factors involved in the induction of the E3 ligases. The amino acid profile of proteins seems to control signalling pathways leading to changes in protein synthesis and proteolysis.
Maize Histone Deacetylase hda101 Is Involved in Plant Development, Gene Transcription, and Sequence-Specific Modulation of Histone Modification of Genes and Repeats[W]

Enzymes catalyzing histone acetylation and deacetylation contribute to the modulation of chromatin structure, thus playing an important role in regulating gene and genome activity. We showed that downregulation and overexpression of the maize (Zea mays) Rpd3-type hda101 histone deacetylase gene induced morphological and developmental defects. Total levels of acetylated histones and histone acetylation of both repetitive and nonrepetitive sequences were affected in hda101 transgenic mutants. However, only transcript levels of genes but not repeats were altered. In particular, hda101 transgenic mutants showed differential expression of genes involved in vegetative-to-reproductive transition, such as liguleless2 and knotted-like genes and their repressor rough sheath2, which are required for meristem initiation and maintenance. Perturbation of hda101 expression also affected histone modifications other than acetylation, including histone H3 dimethylation at Lys-4 and Lys-9 and phosphorylation at Ser-10. Our results indicate that hda101 affects gene transcription and provide evidence of its involvement in setting the histone code, thus mediating developmental programs. Possible functional differences between maize hda101 and its Arabidopsis thaliana ortholog HDA19 are discussed.
Lattices that admit logarithmic worst-case to average-case connection factors

We exhibit an average-case problem that is as hard as finding γ(n)-approximate shortest nonzero vectors in certain n-dimensional lattices in the worst case, for γ(n) = O(√log n). The previously best known factor for any non-trivial class of lattices was γ(n) = Õ(n). Our results apply to families of lattices having special algebraic structure. Specifically, we consider lattices that correspond to ideals in the ring of integers of an algebraic number field. The worst-case problem we rely on is to find approximate shortest vectors in these lattices, under an appropriate form of preprocessing of the number field. For the connection factors γ(n) we achieve, the corresponding decision problems on ideal lattices are not known to be NP-hard; in fact, they are in P. However, the search approximation problems still appear to be very hard. Indeed, ideal lattices are well-studied objects in computational number theory, and the best known algorithms for them seem to perform no better than the best known algorithms for general lattices. To obtain the best possible connection factor, we instantiate our constructions with infinite families of number fields having constant root discriminant. Such families are known to exist and are computable, though no efficient construction is yet known. Our work motivates the search for such constructions. Even constructions of number fields having root discriminant up to O(n2/3-ε) would yield connection factors better than Õ(n). As an additional contribution, we give reductions between various worst-case problems on ideal lattices, showing for example that the shortest vector problem is no harder than the closest vector problem. These results are analogous to previously-known reductions for general lattices.