Miracle-dz/UniFAR-FTUs huggingface dataset:
Darbarer @ AutoMin2023: Transcription simplification for concise minute generation from multi-party conversations

This document reports the approach of our team Darbarer for the main task (Task A) of the AutoMin 2023 challenge. Our system is composed of four main modules. The first module relies on a text simplification model aiming at standardizing the utterances of the conversation and compressing the input in order to focus on informative content. The second module handles summarization by employing a straightforward segmentation strategy and a fine-tuned BART-based generative model. Then a titling module has been trained in order to propose a short description of each summarized block. Lastly, we apply a post-processing step aimed at enhancing readability through specific formatting rules. Our contributions lie in the first, third and last steps. Our system generates precise and concise minutes. We provide a detailed description of our modules, discuss the difficulty of evaluating their impact and propose an analysis of observed errors in our generated minutes.
Transcriptional acclimation to warming temperatures of the Australian alpine herb Wahlenbergia ceracea

Understanding the molecular basis of plant heat tolerance helps to predict the consequences of a warming climate on plant performance, particularly in vulnerable environments. Our current understanding comes primarily from studies in Arabidopsis thaliana and selected crops exposed to short and intense heat stress. In this study we sought to characterise the molecular responses of an Australian alpine herb (Wahlenbergia ceracea) to growth under sustained moderate warming. We compared responses of pre-defined tolerant and sensitive lines, based on measures of photosynthetic stability, to growth under cool or warm temperatures to identify the pathways involved in thermal tolerance and acclimation. Under warmer growth temperatures, W. ceracea up-regulated genes involved in RNA metabolism, while down-regulating those involved in photosynthesis and pigment metabolism. In tolerant lines, genes related to photosystem II, light-dependent photosynthetic reactions, and chlorophyll metabolism were more strongly down-regulated. This suggests that the regulation of electron transport and its components may be involved in thermal acclimation. Our results also highlight the importance of hormonal gene networks, particularly ethylene, during longer-term moderate warming. In conclusion, our results point to post-transcriptional processes and the stabilisation of the electron transport chain as candidate mechanisms for thermal acclimation in W. ceracea. The study also revealed many non-orthologous temperature-responsive genes, whose characterization may enhance our understanding of physiological acclimation and have relevance for the biotechnological improvement of threatened species and crops.
Sia: Heterogeneity-aware, goodput-optimized ML-cluster scheduling

The Sia scheduler efficiently assigns heterogeneous deep learning (DL) cluster resources to elastic resource-adaptive jobs. Although some recent schedulers address one aspect or another (e.g., heterogeneity or resource-adaptivity), none addresses all and most scale poorly to large clusters and/or heavy workloads even without the full complexity of the combined scheduling problem. Sia introduces a new scheduling formulation that can scale to the search-space sizes and intentionally match jobs and their configurations to GPU types and counts, while adapting to changes in cluster load and job mix over time. Sia also introduces a low-profiling-overhead approach to bootstrapping (for each new job) throughput models used to evaluate possible resource assignments, and it is the first cluster scheduler to support elastic scaling of hybrid parallel jobs. Extensive evaluations show that Sia outperforms state-of-the-art schedulers. For example, even on relatively small 44- to 64-GPU clusters with a mix of three GPU types, Sia reduces average job completion time (JCT) by 30--93%, 99th percentile JCT and makespan by 28--95%, and GPU hours used by 12--55% for workloads derived from 3 real-world environments. Additional experiments demonstrate that Sia scales to at least 2000-GPU clusters, provides improved fairness, and is not over-sensitive to scheduler parameter settings.
A chromosome-level reference genome of a Fabaceae species yam bean (Pachyrhizus erosus)

Yam bean (Pachyrhizus erosus L.), belonging to the family Fabaceae, is an important but underutilized root crop. Here, we generated a high-quality chromosome-level reference genome of yam bean by PacBio HiFi and Hi-C sequencing, with assembly size of 539.0 Mb, contig N50 of 25.6 Mb, and BUSCO complete rate of 99.3%. Then, we anchored 94.4% of the contig sequences into 11 pseudo-chromosomes, and assembled the telomeres at 86.4% (19/22) of the chromosome-ends. A total of 44,692 protein-coding genes were predicted, with the BUSCO complete rate of 99.3%, comparable to that of the genome assembly. Compared to the previously reported yam bean genome, the current assembly has a 1,388-fold increase in contig N50 size, and 12.2% and 24.3% increase in BUSCO complete rate for the genome sequence and gene set, respectively. Evolutionary analysis revealed that yam bean diverged from the clade of soybean and Pueraria lobata var. montana 22.5 MYA. This high-quality genome assembly will greatly facilitate the breeding of yam bean based on the genetic and genomic methods.
SCancerRNA: Expression at the Single Cell Level and Interaction Resource of Non-coding RNA Biomarkers for Cancers

Non-coding RNAs (ncRNAs) participate in multiple biological processes associated with cancer as tumor suppressors or oncogenic drivers. Due to their high stability in plasma, urine, and many other fluids, ncRNAs have the potential to serve as key biomarkers for early diagnosis and screening of cancers. During cancer progression, tumor heterogeneity plays a crucial role, and it is particularly important to understand the gene expression patterns of individual cells. With the development of single-cell RNA sequencing (scRNA-seq) technologies, uncovering gene expression in different cell types for human cancers has become feasible by profiling transcriptomes at the cellular level. However, a well-organized and comprehensive online resource that provides access to the expression of genes corresponding to ncRNA biomarkers in different cell types at the single cell level is not available yet. Therefore, we developed the SCancerRNA database to summarize experimentally supported data on long ncRNA (lncRNA), microRNA (miRNA), piwi-interacting RNA (piRNA), small nucleolar RNA (snoRNA), and circular RNA (circRNA) biomarkers, as well as data on their differential expression at the cellular level. Furthermore, we collected biological functions and clinical applications of biomarkers to facilitate the application of ncRNA biomarkers to cancer diagnosis, as well as monitoring of progression and targeted therapies. SCancerRNA also allows users to explore interaction networks of different types of ncRNAs, and build computational models in the future. SCancerRNA is freely accessible at http://www.scancerrna. com/BioMarker.
Removal of heavy liquid separates from glass centrifuge tubes; additional suggestions

Tetrabromoethane, with a freezing point almost 8 degrees C. below that of bromoform, gives greater assurance that the frozen plug with the contained heavy minerals will not loosen and come out of the tube when the light fraction is removed. An additional refinement is to use a tapered rubber stopper that has a glass rod fitted in its top and place this in a tapered centrifuge tube scaling the frozen heavy liquid beneath. The tube can then be washed of any light fraction that may have adhered to the side.
Nutrient colimitation is a quantitative, dynamic property of microbial populations

Resource availability dictates how fast and how much microbial populations grow. Quantifying the relationship between microbial growth and resource concentrations makes it possible to promote, inhibit, and predict microbial activity. Microbes require many resources, including macronutrients (e.g., carbon and nitrogen), micronutrients (e.g., metals), and complex resources like vitamins and amino acids. In nature, many of these resources are scarce and their abundances co-vary. This presents the possibility of resource colimitation, when more than one resource limits growth simultaneously. Despite growing evidence for colimitation, the data is difficult to interpret and compare due to lack of quantitative definitions for limitation and colimitation. In this work, we quantify limitation by individual resources using a limitation coefficient and introduce a colimitation index for measuring the effective number of limiting resources. These quantities demonstrate that limitation conditions are not binary or static, but rather exist on a continuum and can change over time as resource conditions change. Furthermore, they allow us to illustrate how limitation of microbial growth rate and biomass yield are related but distinct notions. To demonstrate these concepts, we measure growth of Escherichia coli under laboratory conditions, which demonstrates that colimitation is readily accessible in clonal populations under these conditions. Finally, we apply our framework to environmental data to provide intuition for what limitation conditions might exist in nature. Altogether our results provide a quantitative framework for understanding and quantifying colimitation in a wide range of microbial systems. SIGNIFICANCE STATEMENT Much of what we know about microbes is from the perspective of a single nutrient limitation, but does this reflect the ecological and evolutionary reality of how microbes live in nature? We present a framework that allows us to assess the extent of nutrient colimitation, providing a quantitative treatment of a problem that is usually interpreted qualitatively. We demonstrate that colimitation of microbial growth rates and biomass yield is relevant in nature and accessible in laboratory conditions, including for clonal populations and independent, elemental resources. This allows us to conclude that the spectrum of microbial growth is best understood in the context of multiple nutrients.
Intrinsic disorder in flaviviral capsid proteins and their role in pathogenesis

A high level of disorder in many viral proteins is a direct consequence of their small genomes, which makes interaction with multiple binding partners a necessity for infection and pathogenicity. A segment of the flaviviral capsid protein, also known as the molecular recognition feature (MoRF), undergoes a disorder-to-order transition upon binding to several protein partners. In order to understand their role in pathogenesis, the MORFs were identified and their homology was studied. Despite the lack of sequence similarities, the docking studies of Cs with the host proteins indicate conserved interactions involving MORFs across members of the phylogenetic subclades. Additionally, it was observed from the protein-protein networks that some MoRFs preferentially bind proteins that are involved in specialized functions such as ribosome biogenesis. The findings point to the importance of the MoRFs in the flaviviral life cycle, with important consequences for disease progression and suppression of the host immune system. Potentially, they might have impacted the way flaviviruses evolved to infect varied hosts using multiple vectors.
Clay mineral records of East Asian monsoon evolution during late Quaternary in the southern South China Sea

High-resolution clay mineral records combined with oxygen isotopic stratigraphy over the past 190 ka during late Quaternary from core MD01-2393 off the Mekong River in the southern South China Sea are reported to reconstruct a history of East Asian monsoon evolution. The dominating clay mineral components indicate a strong glacial-interglacial cyclicity, with high glacial illite, chlorite, and kaolinite contents and high interglacial smectites content. The provenance analysis indicates the direct input of clay minerals via the Mekong River drainage basin. lllite and chlorite derived mainly from the upper reach of the Mekong River, where physical erosion of meta-sedimentary rocks is dominant. Kaolinite derived mainly from active erosion of inhered clays from reworked sediments in the middle reaches. Srnectites originated mainly through bisiallitic soils in the middle to lower reaches of the Mekong River. The smectites/(illite+chlorite) and smectites/kaolinite ratios are determined as mineralogical indicators of East Asian monsoon variations. Relatively high ratios occur during interglacials and indicate strengthened summer-monsoon rainfall and weakened winter-monsoon winds; relatively lower ratios happened in glacials, indicating intensified winter monsoon and weakened summer monsoon. The evolution of the summer and winter monsoons provides an almost linear response to the summer insolation of the Northern Hemisphere, implying an astronomical forcing of the East Asian monsoon evolution.
Verification of regional climates of GISS GCM. Part 1: Winter

Verification is made of the synoptic fields, sea-level pressure, precipitation rate, 200mb zonal wind and the surface resultant wind generated by two versions of the Goddard Institute for Space Studies (GISS) climate model. The models differ regarding the horizontal resolution of the computation grids and the specification of the sea-surface temperatures. Maps of the regional distributions of seasonal means of the model fields are shown alongside maps that show the observed distributions. Comparisons of the model results with observations are discussed and also summarized in tables according to geographic region.
An extended AVHRR 8‐km NDVI dataset compatible with MODIS and SPOT vegetation NDVI data

Daily daytime Advanced Very High Resolution Radiometer (AVHRR) 4‐km global area coverage data have been processed to produce a Normalized Difference Vegetation Index (NDVI) 8‐km equal‐area dataset from July 1981 through December 2004 for all continents except Antarctica. New features of this dataset include bimonthly composites, NOAA‐9 descending node data from August 1994 to January 1995, volcanic stratospheric aerosol correction for 1982–1984 and 1991–1993, NDVI normalization using empirical mode decomposition/reconstruction to minimize varying solar zenith angle effects introduced by orbital drift, inclusion of data from NOAA‐16 for 2000–2003 and NOAA‐17 for 2003–2004, and a similar dynamic range with the MODIS NDVI. Two NDVI compositing intervals have been produced: a bimonthly global dataset and a 10‐day Africa‐only dataset. Post‐processing review corrected the majority of dropped scan lines, navigation errors, data drop outs, edge‐of‐orbit composite discontinuities, and other artefacts in the composite NDVI data. All data are available from the University of Maryland Global Land Cover Facility (http://glcf.umiacs.umd.edu/data/gimms/).
Expression of the insulin-like growth factor 1 receptor (IGF-1R) in breast cancer cells: evidence for a regulatory role of dolichyl phosphate in the transition from an intracellular to an extracellular IGF-1 pathway.

In this study we provide evidence that the low expression of IGF-1R at the cell surface of estrogen-independent breast cancer cells is due to a low rate of de novo synthesis of dolichyl phosphate. The analyses were performed on the estrogen receptor-negative breast cancer cell line MDA231 and, in comparison, the melanoma cell line SK-MEL-2, which expresses a high number of plasma membrane-bound IGF-1R. Whereas the MDA231 cells had little or no surface expression of IGF-1R, they expressed functional (i.e., ligand-binding) intracellular receptors. By measuring the incorporation of [3H]mevalonate into dolichyl phosphate, we could demonstrate that the rate of dolichyl phosphate synthesis was considerably lower in MDA231 cells than in SK-MEL-2 cells. Furthermore, N-linked glycosylation of the alpha-subunit of IGF-1R was 8-fold higher in the melanoma cells. Following addition of dolichyl phosphate to MDA231 cells, N-linked glycosylation of IGF-1R was drastically increased, which in turn was correlated to a substantial translocation of IGF-1R to the plasma membrane, as assayed by IGF-1 binding analysis and by Western blotting of plasma membrane proteins. The dolichyl phosphate-stimulated receptors were proven to be biochemically active since they exhibited autophosphorylation. Under normal conditions MDA231 cells, expressing very few IGF-1R at the cell surface, were not growth-arrested by an antibody (alphaIR-3) blocking the binding of IGF-1 to IGF-1R. However, after treatment with dolichyl phosphate, leading to a high cell surface expression of IGF-1R, alphaIR-3 efficiently blocked MDA231 cell growth. Taken together with the fact that the breast cancer cells produce IGF-1 and exhibit intracellular binding, our data suggest that the level of de novo -synthesized dolichyl phosphate may be critical for whether the cells will use an intracellular or an extracellular autocrine IGF-1 pathway.
Revealing unexpected complex encoding but simple decoding mechanisms in motor cortex via separating task-relevant neural signals

In motor cortex, task-relevant neural responses are entangled with irrelevant signals, which complicates the study of encoding and decoding mechanisms. It remains unclear whether task-irrelevant signals could conceal some critical truth. One solution is to accurately separate task-relevant and irrelevant signals, but this approach remains elusive due to the unknown ground truth of task-relevant signals. Therefore, we propose a framework to define, extract, and validate task-relevant signals. Analyzing separated signals in three monkeys performing different reaching tasks, we found neural responses previously considered useless encode rich task information in complex nonlinear ways. These responses are critical for neuronal redundancy and reveal movement behaviors occupy a higher-dimensional neural space than previously expected. Surprisingly, when incorporating often-ignored neural dimensions, task information can be decoded linearly as accurately as nonlinear decoding, suggesting linear readout is performed in motor cortex. Our findings prompt that separating task-relevant signals may help uncover more hidden cortical mechanisms.
Privacy in the metaverse : Regulating a complex social construct in a virtual world

Second Life by many is considered to be more than just a game. It is a social microcosmos in which fairly normal people behave normally and where (complex) social behaviour develops. As such it is an interesting environment to study social and legal phenomena. In this chapter we will look at the privacy and how privacy is regulated within Second Life. The analysis will point out shortcomings of the current mode of governance within Second Life and point at near future changes therein. 1 From Snow Crash to EPIC yearbook In 1992, some years before the Internet entered the sphere of ordinary people, Neil Stephenson published the sci-fi novel Snow Crash. In this book, Stephenson sketches a bleak future where the US government is almost completely replaced by private organizations and entrepreneurs who run sovereign suburban enclaves, ‘Burbclaves’. Other notable features of Stephenson's projection are the perfection of pizza delivery, finally, by ‘pizza deliverators’ – pizza delivery guy meets Terminator – and that people, besides taking drugs (the title's Snow Crash), have found distraction in the Metaverse. The Metaverse is a computer generated 3D environment where the players move around as Avatars. Central to the Metaverse is ‘the Street' which is '. subject to development. Developers can build their own small streets feeding off the main one. They can build buildings, parks, signs, as well as things that do not exist in Reality, such as vast hovering overhead light shows, special neighbourhoods where the rules of three dimensional spacetime are ignored, and free combat zones where people can go to hunt and kill each other. ’ [1, p.23]. Snow Crash is an interesting novel, not only because it inspired Linden Lab to model what is now known as Second Life (SL) on the Metaverse, but also because of the model of governance it offers. The novel depicts a world void of the governance structures common to the Western world. Instead, it shows a libertarian society where traditional government responsibilities are subsumed by corporations and private interest, both offline and online (the Metaverse). Interestingly, Second Life is slowly moving to such a model of governance, where the corporation Linden Lab governs the 1 http://www.usatoday. com/printedition/money/20070205/secondlife_cover. art.htm
ARID1A governs the silencing of sex-linked transcription during male meiosis in the mouse

We present evidence implicating the BAF (BRG1/BRM Associated Factor) chromatin remodeler in meiotic sex chromosome inactivation (MSCI). By immunofluorescence (IF), the putative BAF DNA binding subunit, ARID1A (AT-rich Interaction Domain 1a), appeared enriched on the male sex chromosomes during diplonema of meiosis I. Those germ cells showing a Cre-induced loss of ARID1A were arrested in pachynema and failed to repress sex-linked genes, indicating a defective MSCI. Consistent with this defect, mutant sex chromosomes displayed an abnormal presence of elongating RNA polymerase II coupled with an overall increase in chromatin accessibility detectable by ATAC-seq. By investigating potential mechanisms underlying these anomalies, we identified a role for ARID1A in promoting the preferential enrichment of the histone variant, H3.3, on the sex chromosomes, a known hallmark of MSCI. Without ARID1A, the sex chromosomes appeared depleted of H3.3 at levels resembling autosomes. Higher resolution analyses by CUT&RUN revealed shifts in sex-linked H3.3 associations from discrete intergenic sites and broader gene-body domains to promoters in response to the loss of ARID1A. Several sex-linked sites displayed ectopic H3.3 occupancy that did not co-localize with DMC1 (DNA Meiotic Recombinase 1). This observation suggests a requirement for ARID1A in DMC1 localization to the asynapsed sex chromatids. We conclude that ARID1A-directed H3.3 localization influences meiotic sex chromosome gene regulation and DNA repair.
Thermal regime of a headwater stream within a clear‐cut, coastal British Columbia, Canada

This study examined the thermal regime of a headwater stream within a clear‐cut. The stream had a complex morphology dominated by step–pool features, many formed by sediment accumulation upstream of woody debris. Maximum daily temperatures increased up to 5 °C after logging, and were positively associated with maximum daily air temperature and negatively with discharge. Maximum daily temperatures generally increased with downstream distance through the cut block, but decreased with distance in two segments over distances of tens of metres, where the topography indicated relatively concentrated lateral inflow. Localized cool areas within a step–pool unit were associated with zones of concentrated upwelling. Bed temperatures tended to be higher and have greater ranges in areas of downwelling flow into the bed. Heat budget estimates were made using meteorological measurements over the water surface and a model of net radiation using canopy characteristics derived from fisheye photography. Heat exchange driven by hyporheic flow through the channel step was a cooling effect during daytime, with a magnitude up to approximately 25% that of net radiation during the period of maximum daytime warming. Heat budget calculations in these headwater streams are complicated by the heterogeneity of incident solar radiation and channel geometry, as well as uncertainty in estimating heat and water exchanges between the stream and the subsurface via hyporheic exchange and heat conduction. Copyright © 2005 John Wiley & Sons, Ltd.