Miracle-dz/UniFAR-FTUs huggingface dataset:
Eavesdropping on oxygen metabolism

Oxygen—odorless, colorless, and tasteless—makes up about 65% of the human body.1 Oxygen regulates all of the human body’s functions. For example, it energizes our cells, fights aging, and burns up toxins. In fact, almost all diseases are linked to abnormal oxygen metabolism. Cancers are especially starved for oxygen, so measuring tissue oxygenation is a key tool in cancer diagnosis and prognosis.2, 3 At a very early stage of carcinogenesis, epithelial (i.e., inner lining) cells become hyperproliferative and consume much more oxygen to maintain their fast growth.4 This hypermetabolism of oxygen is a hallmark of early stage cancer.5 The ability to accurately map oxygen metabolism would be useful for early cancer detection, which greatly increases the success rate of treatment and hence also the chances of patients’ survival.6 The metabolic rate of oxygen (MRO2/ directly reflects actual oxygen consumption instead of static oxygen concentration, so it is a superior oxygenation index of biological tissue compared to other existing indices (oxygen saturation of hemoglobin sO2, and partial oxygen pressure pO2/. MRO2 can quantify cancer hypermetabolism and brain functions in absolute units. Current techniques for MRO2 quantification, such as positron emission tomography and functional magnetic resonance imaging, either lack the needed spatial resolution for studying the microenvironment of tumors, rely on radioactively labeled exogenous tracers, or both.8 We have developed label-free metabolic photoacoustic microscopy (mPAM) with capillary resolution to quantify MRO2 noninvasively in vivo in absolute units.9 The mPAM technique provides a means to measure optical contrast ultrasonically through the photoacoustic (PA) effect by pinpointing the microvasculature, exciting the hemoglobin molecules with a laser, and then listening to the sound generated by the excited molecules (see Figure 1a). The method is unique Figure 1. (a) Schematic of metabolic photoacoustic microscopy (mPAM) system. A transverse resolution of 5 m and an axial resolution of 15 m are achieved. AL: Acoustic lens; UT: Ultrasonic transducer; WT: Water tank; MS: Motorized scanner. (b) Total concentration of hemoglobin (CHb/ in a mouse ear by mPAM. Scale bar: 500 m. (c) Magnified mPAM of area in dash box in (b) of the oxygen saturation, sO2, and (d) blood flow. Scale bar: 125 m.
ON A PROBLEM OF SCHINZEL

Using elementary methods, A. Schinzel and W. Sierpinski obtained some results concerning the distribution of the Euler function (n) and the function σ(n) which represents the sum of divisors of n. Professor Hua Loo-Keng pointed firstly that about the function (n), we may obtain much more elaborate results by Brun’s method. According to his suggestion, Wang Yuan obtained the results about the function (n) which is better than the results of A. Schinzel and W. Sierpinski. Professor Min Szu-Hoa pointed to me that the Brun’s method may also be used to solve the problem of Schinzel about the function r(n) We obtained Theorem l. For every positive integer k and every sequence of positive integers δ_0, δ_1, … ,δ_(k-1), there exists a natural number n such that δ_v≤(n+v)≤c_0δ_v (v=0, 1, …, k-1) (1) where c_0=c_0(k) is a positive constant. More precisely, if we denote by N(X) the number of integers n in the interval 1 ≤ n≤ X satisfying (1), then for sufficiently large X, we haveN(X)c＇x/log~k X,(2) where c＇=c＇(k; δ_0, … , δ_(k-1)) is a positive constant. Theorem 2. For every positive integer k and every sequence of positive real numbers B_0,B_1,…, B(k-1), there exists a natural number n such that c_1B_v≤r(n+v)/r(n+v+1)≤ c_2 B_v(v=0, 1,…,k-1),(3) where c_1=c_1(k) and c_2=c_2(k) are positive constants. More precisely, if we denote by N~*(X)the number of integers n in the interval 1 ≤n≤X satisfying(3), then for sufficiently large X, we have N~*(X)c~* X/log~(k+1)X, where c~*=c~*(k; B_0, B_1, …, B(k-1)) is a positive constant. I have been informed that these theorems were also proved by Schinzel independently and Wang Yung and Schinzel will publish a joint paper (to be appear in Bulletin de l’Academie Polonaise des Sciences), containing these theorems. The method of this paper may be applied to the function Ts(n)=
The intertextuality of argumentation: a semiotic approach to academic writing in higher education

Abstract The importance of argumentation in academic writing, while historically recognised, has arguably lost prominence alongside the rapid expansion of higher education since the early 1990s in the UK. This has been exacerbated by an increasingly prevalent technological intervention in teaching and learning processes. With this as a background, this article presents a semiotic analysis of student dissertation extracts to illustrate the role of intertextuality in governing interpretative, evaluative, and concluding propositions in argumentation. Each proposition is perceived as indexed to syntactical compositionality by which a previous proposition elicits a present one that awaits a future one, thus forming a line of argument. The analysis teases out what is at stake concerning the interdependence of signifying codes in textual relations and functions. This brings into view a network of sign actions that lends itself to instances of signification in mediating and coordinating propositions in argumentation. The article concludes with reflection on the medium of English as a lingua franca for studies in higher education, highlighting a semiotic understanding of the intertextuality of argumentation in academic writing.
Orientation dependent annealing kinetics of ion tracks in c-SiO2

The structure and thermal response of amorphous ion tracks formed along the [112¯0], [101¯0], and [0001]-directions in crystalline quartz have been investigated using small angle x-ray scattering. The radii of the ion tracks vary by about 5% (0.3 nm) for tracks along different crystallographic directions. Molecular dynamics simulations reproduce this anisotropy along the [101¯0] and [0001] directions and suggest that differences in thermal conductivity along these directions are partly responsible for this observation. Using in situ annealing, tracks along the [101¯0] and [0001] directions were shown to recrystallize during thermal annealing around 960–1020 °C with activations energies around 6 eV, while those along the [112¯0]-direction already disappeared at 640 °C with a significantly lower activation energy around 3–4 eV.
Change in global burden of unintentional drowning from 1990 to 2019 and its association with social determinants of health: findings from the Global Burden of Disease Study 2019

Objective To systematically analyse global, regional and national burden change of unintentional drowning from 1990 to 2019, and to further quantify the contribution of social determinants of health (SDH) on the change. Design Data from the Global Burden of Disease Study 2019 were used in this study. Setting and participants Individuals of all ages and genders from 204 countries and territories. Main outcome measures The main outcomes were the age-standardised rates (ASRs) of mortality and disability-adjusted life-years (DALYs) of unintentional drowning. The percentage change in the ASRs were used to estimate the joint effect of SDH on trends in global burden of drowning. Results We observed that the global burden of unintentional drowning declined markedly from 1990 to 2019, with age-standardised mortality rate and DALYs rate decreasing by 61.5% and 68.2%, respectively. Women, children, middle Socio-Demographic Index (SDI) countries, South-East Asia and Western Pacific region had higher reduction. At national level, greater reductions were observed in Armenia and Republic of Korea, but significant increases in Cabo Verde and Vanuatu. We found that every one percentile increase in six SDHs (Gross Domestic Product (GDP) per person, SDI, educational attainment, health spending, health workers and urbanisation) was associated with a decrease of 0.15% and 0.16% in drowning age-standardised mortality rate and DALYs rate globally, respectively. Health spending and GDP per capita were the main contributors to the reduction of drowning globally. Conclusions The global burden of unintentional drowning significantly declined in the past three decades, and the improvement of SDHs such as GDP per capita and health spending mainly contributed to the decrease. Our findings indicate that improvement of SDHs is critical for drowning prevention and control.
Trees in Polyhedral Graphs

A graph is said to be d-polyhedral provided it is isomorphic with the graph formed by the vertices and edges of a d-dimensional bounded (convex) polyhedron (d-polyhedron). A k-tree is a connected acyclic graph in which each vertex is of valence ⩽k.
PS 813: Multivariate Statistical Inference Spring 2013

Effective participation in the social sciences requires familiarity with the basic elements of multivariate statistics. As social scientists rarely have the opportunity to study phenomena or behavior through controlled experiments, empirical tests of hypotheses derived from theory must often be coaxed either from data collected without the benefit of random assignment or from data that "happen" to be available as a byproduct of some non-research process. It is usually necessary, therefore, to use multivariate techniques to attempt to control statistically for at least those observable factors that cannot be controlled by random assignment. Absent familiarity with these basic techniques, social scientists cannot critically evaluate empirical results in their substantive areas of interest. Without some facility for actually using the techniques, they are less likely to be able to contribute in an important way to the testing of theory or even to the description of complicated phenomena.
High methane flux in a tropical peatland post-fire is linked to homogenous selection of diverse methanogenic archaea

Tropical peatlands in South-East Asia are some of the most carbon dense ecosystems in the world. Recurrent wildfires in repurposed peatlands release massive amounts of carbon and other greenhouse gases, strongly alter peat geochemistry and physicochemical conditions. However, little is known about the impact of fire on peat microbiome composition, microbial guilds contributing to greenhouse gas emissions, and their predictability based on environmental conditions. Here, we address this gap by studying peat microbiomes from fire-affected and intact areas of a tropical peatland in Brunei using high-throughput sequencing and ecological process modelling at the community and clade levels. We show that fire disrupts depth-stratification of peat microbiomes with the strongest effects observed at 1m below the surface. The enrichment of specific taxa and methanogenic archaea at such depths suggests an adaptation to low-energy conditions post-fire. Finally, fire shifts archaeal community composition and clades containing abundant methanogens in a homogeneous manner that can be predicted from environmental conditions and functional traits. Together, our findings provide a biological basis for earlier work which reported elevated methane flux 2-3 years post-fire and show that such changes follow predictable trajectories with important implications for post-fire microbiome forecasting and ecosystem recovery efforts.
Hormonal coordination of peripheral motor output and corollary discharge in a communication system

Steroid hormones remodel neural networks to induce developmental or seasonal changes in animal behavior, but little is known about hormonal modulation of sensorimotor integration. Here, we investigate hormonal effects on a predictive motor signal, termed corollary discharge, that modulates sensory processing in weakly electric mormyrid fish. In the electrosensory pathway mediating communication behavior, inhibition activated by a corollary discharge precisely blocks sensory responses to self-generated electric pulses, allowing the downstream circuit to selectively analyze communication signals from nearby fish. These electric pulses are elongated by increasing testosterone levels in males during the breeding season. Using systematic testosterone treatment, we induced electric-pulse elongation in fish and found that the timing of electroreceptor spiking responses to self-generated pulses (reafference) was delayed as electric pulse duration increased. Recording evoked potentials from a midbrain electrosensory nucleus revealed that the timing of corollary discharge inhibition was delayed and elongated by testosterone. Further, this shift in corollary discharge timing was precisely matched to the shift in timing of the reafferent spikes. We then asked whether the shift in inhibition timing was caused by direct action of testosterone on the corollary discharge circuit or plasticity of the circuit through altered sensory feedback. We surgically silenced the electric organs of fish and found similar hormonal modulation of corollary discharge timing between intact and silent fish, suggesting that sensory feedback was not required for this shift. These results demonstrate that testosterone directly and independently modulates peripheral motor output and a predictive motor signal in a coordinated manner. Significance Self-other discrimination is essential for animals. Internal predictive motor signals, or corollary discharge, provide motor information to sensory areas so that animals can perceive self- and other-generated stimuli differently. As behavior and associated sensory feedback change with development, corollary discharge must adjust accordingly. Using weakly electric mormyrid fish, we show that the steroid hormone testosterone alters electric signaling behavior and the resulting sensory feedback, as well as the timing of corollary discharge, to precisely match the altered sensory feedback. We also found that the altered sensory feedback itself is not necessary to drive this corollary discharge modulation. Our findings demonstrate that testosterone directly and independently regulates peripheral motor output and corollary discharge in a coordinated manner.
Direct monitoring of the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization from gaps and overhangs

Hybridization of short nucleic acid segments (<4 nucleotides) to single-strand templates occurs as a critical intermediate in processes such as non-enzymatic nucleic acid replication and toehold-mediated strand displacement. These templates often contain adjacent duplex segments that stabilize base pairing with single-strand gaps or overhangs, but the thermodynamics and kinetics of hybridization in such contexts are poorly understood due to experimental challenges of probing weak binding and rapid structural dynamics. Here we develop an approach to directly measure the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization using steady-state and temperature-jump infrared spectroscopy. Our results suggest that dinucleotide binding is stabilized through coaxial stacking interactions with the adjacent duplex segments as well as from potential non-canonical base pairing configurations and structural dynamics of gap and overhang templates revealed using molecular dynamics simulations. We measure timescales for dissociation ranging from 0.2 to 40 µs depending on the template and temperature. Dinucleotide hybridization and dehybridization involves a significant free energy barrier with characteristics resembling that of canonical oligonucleotides. Together, our work provides an initial step for predicting the stability and kinetics of hybridization between short nucleic acid segments and various templates.
Next Generation Datacenter Architecture

Next Generation Datacenter Architecture by Xiang Gao Doctor of Philosophy in Computer Science University of California, Berkeley Professor Sylvia Ratnasamy, Co-chair Professor Scott Shenker, Co-chair Modern datacenters are the foundation of large scale Internet services, such as search engines, cloud computing and social networks. In this thesis, I will investigate the new challenges in building and managing large scale datacenters. Specifically, I will show trends and challenges in the software stack, the hardware stack and the network stack of modern datacenters, and propose new approaches to cope with these challenges. In the software stack, there is a movement to serverless computing where cloud customers can write short-lived functions to run their workloads in the cloud without the hassle of managing servers. Yet the storage stack has not changed to accommodate serverless workloads. We build a storage system called Savanna that significantly improves the serverless applications performance. In the hardware stack, with the end of Moore’s Law, researchers are proposing disaggregated datacenters with pools of standalone resource blades. These resource blades are directly connected by the network fabric, and I will present the requirements of building such a network fabric. Lastly, in the network stack, new congestion control algorithms are proposed (e.g. pFabric) to reduce the flow completion time. However, these algorithms require specialized hardware to achieve desirable performance. I designed pHost, a simple end-host based congestion control scheme that has comparable performance with pFabric without any specialized hardware support.
Elevated temperatures reduce population-specific transcriptional plasticity in developing lake sturgeon (Acipenser fulvescens)

Rising mean and variance in temperatures elevate threats to endangered freshwater species such as lake sturgeon, Acipenser fulvescens. Previous research demonstrated that higher temperatures during development result in physiological consequences for lake sturgeon populations throughout Manitoba, Canada, with alteration of metabolic rate, thermal tolerance, transcriptional responses, growth, and mortality. We acclimated lake sturgeon (30 – 60 days post fertilization, a period of high mortality) from northern and southern populations (56° 02′ 46.5″ N, 96° 54′ 18.6″ W and 50° 17′ 52″ N, 95° 32′ 51″ W respectively, separated by approximately 650 km) within Manitoba to current (summer highs of 20-23°C) and future projected (+2-3°C) environmental temperatures of 16, 20, and 24°C for 30 days, and measured gill transcriptional responses using RNAseq. Transcripts revealed SNPs consistent with genetically distinct populations and transcriptional responses altered by acclimation temperature. There were a higher number of differentially expressed transcripts observed in the southern, compared to the northern, population as temperatures increased, indicating enhanced transcriptional plasticity. Both lake sturgeon populations responded to elevated acclimation temperatures by downregulating the transcription of genes involved in protein synthesis and energy production. Further, there were population-specific thresholds for the downregulation of processes promoting transcriptional plasticity as well as mitochondrial function as the northern population showed decreases at 20°C, while this capacity was not diminished until 24°C in the southern population. These transcriptional responses highlight the molecular impacts of increasing temperatures for divergent lake sturgeon populations during vulnerable developmental periods and the critical influence of transcriptome plasticity on acclimation capacity.
Single-cell DNA replication dynamics in genomically unstable cancers

Dysregulated DNA replication is both a cause and a consequence of aneuploidy, yet the dynamics of DNA replication in aneuploid cell populations remains understudied. We developed a new method, PERT, for inferring cell-specific DNA replication states from single-cell whole genome sequencing, and investigated clone-specific DNA replication dynamics in >50,000 cells obtained from a collection of aneuploid and clonally heterogeneous cell lines, xenografts and primary cancer tissues. Clone replication timing (RT) profiles correlated with future copy number changes in serially passaged cell lines. Cell type was the strongest determinant of RT heterogeneity, while whole genome doubling and mutational process were associated with accumulation of late S-phase cells and weaker RT associations. Copy number changes affecting chromosome X had striking impact on RT, with loss of the inactive X allele shifting replication earlier, and loss of inactive Xq resulting in reactivation of Xp. Finally, analysis of time series xenografts illustrate how cell cycle distributions approximate clone proliferation, recapitulating expected relationships between proliferation and fitness in treatment-naive and chemotherapeutic contexts.
Mesenchymal stem cells therapy for acute kidney injury: A systematic review with meta-analysis based on rat model

Objective: To systematically evaluate the efficacy of mesenchymal stem cells (MSCs) for acute kidney injury (AKI) in preclinical studies and to explore the optimal transplantation strategy of MSCs by network meta-analysis with the aim of improving the efficacy of stem cell therapy. Methods: Computer searches of PubMed, Web of Science, Cochrane, Embase, CNKI, Wanfang, VIP, and CBM databases were conducted until 17 August 2022. Literature screening, data extraction and quality evaluation were performed independently by two researchers. Results and Discussion: A total of 50 randomized controlled animal studies were included. The results of traditional meta-analysis showed that MSCs could significantly improve the renal function and injured renal tissue of AKI rats in different subgroups. The results of network meta-analysis showed that although there was no significant difference in the therapeutic effect between different transplant routes and doses of MSCs, the results of surface under the cumulative ranking probability curve (SUCRA) showed that the therapeutic effect of intravenous transplantation of MSCs was better than that of arterial and intrarenal transplantation, and the therapeutic effect of high dose (>1×106) was better than that of low dose (≤1×106). However, the current preclinical studies have limitations in experimental design, measurement and reporting of results, and more high-quality studies, especially direct comparative evidence, are needed in the future to further confirm the best transplantation strategy of MSCs in AKI. Systematic Review Registration: identifier https://CRD42022361199, https://www.crd. york.ac. uk/prospero.