Miracle-dz/UniFAR-FTUs huggingface dataset:
1‐O‐alkenyl‐sn‐glyceryl‐3‐phosphorylcholine may be a novel posttranslational modification used by the placenta

Neurokinin B (NKB) secreted by the placenta was previously found to be raised in preeclampsia and most of the symptoms in this disease appeared to be through progressive activation of the three neurokinin receptors. Further characterization of placental NKB revealed that placental NKB eluted in the approximate position of a 13mer and this was confirmed by TOF mass spectrometry which gave a mass of 1580. Although this is consistent with dimethylated NKB‐Gly‐Lys‐Arg, further characterization (immunological and mass spectrometric fragment analysis) suggested a novel posttranslational modification containing phosphocholine (PC) with some evidence for glycerol and a coordinated alkene. The structure that fits all the data is that a form of platelet activating factor is attached to the aspartyl side chain at position 4 of NKB and thus now implicates placental NKB in the platelet pathology seen in preeclampsia. As it has been reported that it is the PC group per se attached to certain proteins secreted by filarial nematodes imparts them with immune inhibitory properties and thus survival in the host over long periods, attaching PC to placental secretory peptide hormones (also be found on the placental precursors of CRF, ACTH, and activin) may result in a similar situation. © 2010 Wiley Periodicals,Inc. Biopolymers (Pept Sci) 96: 189–192, 2011.
Different contributions of ASIC channels 1a, 2, and 3 in gastrointestinal mechanosensory function

Aims: Members of the acid sensing ion channel (ASIC) family are strong candidates as mechanical transducers in sensory function. The authors have shown that ASIC1a has no role in skin but a clear influence in gastrointestinal mechanotransduction. Here they investigate further ASIC1a in gut mechanoreceptors, and compare its influence with ASIC2 and ASIC3. Methods and results: Expression of ASIC1a, 2, and 3 mRNA was found in vagal (nodose) and dorsal root ganglia (DRG), and was lost in mice lacking the respective genes. Recordings of different classes of splanchnic colonic afferents and vagal gastro-oesophageal afferents revealed that disruption of ASIC1a increased the mechanical sensitivity of all afferents in both locations. Disruption of ASIC2 had varied effects: increased mechanosensitivity in gastro-oesophageal mucosal endings, decreases in gastro-oesophageal tension receptors, increases in colonic serosal endings, and no change in colonic mesenteric endings. In ASIC3-/- mice, all afferent classes had markedly reduced mechanosensitivity except gastro-oesophageal mucosal receptors. Observations of gastric emptying and faecal output confirmed that increases in mechanosensitivity translate to changes in digestive function in conscious animals. Conclusions: These data show that ASIC3 makes a critical positive contribution to mechanosensitivity in three out of four classes of visceral afferents. The presence of ASIC1a appears to provide an inhibitory contribution to the ion channel complex, whereas the role of ASIC2 differs widely across subclasses of afferents. These findings contrast sharply with the effects of ASIC1, 2, and 3 in skin, suggesting that targeting these subunits with pharmacological agents may have different and more pronounced effects on mechanosensitivity in the viscera.
Algal endosymbionts as vectors of horizontal gene transfer in photosynthetic eukaryotes

Photosynthesis in eukaryotes occurs in the plastid, an organelle that is derived from a single cyanobacterial primary endosymbiosis in the common ancestor of the supergroup Plantae (or Archaeplastida) that includes green, red, and glaucophyte algae and plants. However a variety of other phytoplankton such as the chlorophyll c-containing diatoms, dinoflagellates, and haptophytes contain a red alga-derived plastid that traces its origin to secondary or tertiary (eukaryote engulfs eukaryote) endosymbiosis. The hypothesis of Plantae monophyly has only recently been substantiated, however the extent and role of endosymbiotic and horizontal gene transfer (EGT and HGT) in algal genome evolution still remain to be fully understood. What is becoming clear from analysis of complete genome data is that algal gene complements can no longer be considered essentially eukaryotic in provenance; i.e., with the expected addition of several hundred cyanobacterial genes derived from EGT and a similar number derived from the mitochondrial ancestor. For example, we now know that foreign cells such as Chlamydiae and other prokaryotes have made significant contributions to plastid functions in Plantae. Perhaps more surprising is the recent finding of extensive bacterium-derived HGT in the nuclear genome of the unicellular red alga Porphyridium purpureum that does not relate to plastid functions. These non-endosymbiont gene transfers not only shaped the evolutionary history of Plantae but also were propagated via secondary endosymbiosis to a multitude of other phytoplankton. Here we discuss the idea that Plantae (in particular red algae) are one of the major players in eukaryote genome evolution by virtue of their ability to act as “sinks” and “sources” of foreign genes through HGT and endosymbiosis, respectively. This hypothesis recognizes the often under-appreciated Rhodophyta as major sources of genetic novelty among photosynthetic eukaryotes.
Power to the People: energy in Europe over the last five centuries

sputtering and struggling, through the 1950s and 1960s. (See Andre Beteille, Universities at the Crossroads (Delhi, 2010), for the bigger picture. ) The central and strongest section of the book deals with the development of agricultural research in colonial India after the establishment of the Pusa Institute, but especially after the Royal Commission on Agriculture reported in 1928. Again, anticipating patterns that solidified after Indian independence, the central government took on technical support and guidance, as well as strategic funding, while actual schemes and institutions were created in the provinces. Just two years earlier, Albert Howard had chaired the Indian Science Congress in 1926 and declared that the flow of learning between scientists and farmers would need to be a two-way process for agriculture to flourish, with due respect afforded to the lands and cultures expected to nourish it. (See Wendell Berry, ‘Introduction’ in Albert Howard, The Soil and Health: A Study of Organic Agriculture (Lexington, 2007), for a brief overview of Howard’s philosophy and misgivings about privileging modern science at the expense of farmer knowledge. ) But by the 1930s, Indian agriculture’s fate had been left in the hands of an increasingly imperious and impatient scientific agenda, and this approach – committed to modern plant and animal breeding, mechanization and chemicals – continued even more rapidly and on a grander scale after 1950. Surendra Mohan Mishra evinces interest in the environmental consequences of agriculture and provides some valuable information on pollution, the disruption of river hydrology and other baneful effects. However, the opportunity to assess coherently the damaging course that was set, even by the late 1940s, as the ship of Indian agriculture sailed towards modernization, is not seized in this study. Instead the author recoups, in a not very original fashion, some of the writing on environmentalism and nature love in Indian traditions, and does not relate that discussion to the question of modern agriculture that was actually consuming the central legislature and parliament in the 1940s and 1950s. The book concludes rather oddly with a list of twenty observations, some of which are tantalizing, if obscure and cryptic. The promise of examining the passage of agricultural policy and legislative debate from the realm of colonial power over land to a free nation’s commitments to democracy and fundamental rights remains unrealized in any sophisticated analytical sense, but the voluminous information provided in this book will be of great use to interested readers. It certainly confirms the author’s instinct, and that of much other recent scholarship, that there were strong continuities in policy and institutions across the colonial/postcolonial divide in India, in agriculture, as in other areas of economic and social development. K. Sivaramakrishnan Yale University kalyanakrishnan.sivaramakrishnan@yale.edu
The effects of code-based literacy interventions on spelling achievement: A meta-analysis

In this study, we used meta-analysis to quantitatively assess the effects of systematic code-based literacy interventions on spelling achievement. Studies included in the meta-analysis were published in English, involved a code-based literacy intervention in a school setting, included a control or comparison group, measured spelling as an outcome at post-test, and reported sufficient statistics to compute effect sizes. Random effects analysis models were based on 91 studies and 153 computed effect sizes. The mean effect size for all studies was moderate, d = 0.58, 95% CI [. 49, . 68], indicating that systematic code-based literacy instruction is more effective at improving spelling outcomes than non-code-based or less systematic instruction. The total sample size was 9,046 participants in pre-school to grade 11.
An Aerobic Weight-Loaded Pilot Exercise Intervention for Breast Cancer Survivors: Bone Remodeling and Body Composition Outcomes

Objective. Weight gain and bone loss are commonly reported in breast cancer survivors. The purpose of this pilot study is to assess feasibility and explore the effect of an aerobic weight-loaded exercise intervention on bone remodeling, weight, and body composition. Design. A one-group pre-posttest design was used to test a 16—24-week supervised walking exercise intervention among women within 2 years of menopause. Through Weeks 1—4, time and weight were progressively increased. By Week 5 and through the end of the intervention, a waist belt was loaded with 5 lb and participants spent 45 min on the treadmill 3 times/week. Bone remodeling was measured by serum biomarkers (N-terminal propeptides of type I collagen [NTX] and serum osteocalcin). Dual-energy absorptiometry scans assessed body composition. Data were collected at baseline and 16 and 24 weeks. Results. The majority of the 26 participants were married, well educated, and employed, with a mean age of 51.3 years (SD = 6.2). The high adherence (M = 88.2%, SD = 6.8) demonstrated feasiblity. There were no significant changes in serum osteocalcin (p = .67), serum NTX (p = .31), lean muscle mass (p = .08), or percent fat mass for the group as a whole (p = .14), but fat mass increased for women on adjuvant endocrine therapy (p = .04). The women maintained their weight. Conclusions. This novel exercise intervention for breast cancer survivors was feasible, and women otherwise at high risk for weight gain and bone loss maintained their weight and bone mass.
Similar, but not identical, modulation of expression of extracellular matrix components during in vitro and in vivo aging of human skin fibroblasts

Regulation of the synthesis of procollagen and other extracellular matrix components was examined in human skin fibroblasts obtained from donors of various ages, from fetal to 80 years old (in vivo aged), and in fetal fibroblasts at varying passage levels (in vitro aged). Growth rates and saturation densities of fibroblasts decreased with increasing age of the donor and after passage 20 of fetal fibroblasts. The rates of collagen and proteoglycan synthesis also decreased during both types of aging to about 10–25% of the rate in early passage fetal fibroblasts, whereas the synthesis of total noncollagenous proteins was not greatly affected. Decreased collagen synthesis in both types of aging was correlated with lower steady‐state levels of mRNAs for the two subunits of type I procollagen mRNA, although their regulation was not coordinate. Type III collagen mRNA levels also declined in both types of aging. The concentration of fibronectin mRNA also decreased during in vitro aging but more rapidly than the collagen mRNAs, whereas in fibroblasts from 51–80‐year‐old donors, it was similar to or higher than in early passage fetal fibroblasts. This study suggests that the decreased synthesis of procollagen and proteoglycans in in vivo aged fibroblasts represents changes that are responsible for intrinsic degenerative changes that occur in human skin during aging. Furthermore, although in vitro and in vivo aging were similar in many respects, they were not equivalent, as evidenced by the differences in regulation of fibronectin expression. © 1992 Wiley‐Liss, Inc.
Bayesian point pattern matching for linear transformations

We introduce a novel Bayesian inexact point pattern matching model that assumes that a linear transformation relates the two sets of points. The matching problem is inexact due to the lack of one-to-one correspondence between the point sets and the presence of noise. The algorithm is itself inexact; we use variational Bayesian approximation to estimate the posterior distributions in the face of a problematic evidence term. The method turns out to be similar in structure to the iterative closest point algorithm.
Optimizing I/O for Big Array Analytics

Big array analytics is becoming indispensable in answering important scientific and business questions. Most analysis tasks consist of multiple steps, each making one or multiple passes over the arrays to be analyzed and generating intermediate results. In the big data setting, I/O optimization is a key to efficient analytics. In this paper, we develop a framework and techniques for capturing a broad range of analysis tasks expressible in nested-loop forms, representing them in a declarative way, and optimizing their I/O by identifying sharing opportunities. Experiment results show that our optimizer is capable of finding execution plans that exploit nontrivial I/O sharing opportunities with significant savings.
Time–frequency modelling and discrimination of noise in the electrocardiogram

In widely spread home care applications of ECG recorders, the traditional approach to the problem of noise immunity is no longer sufficient. This paper presents a new ECG-dedicated noise removal technique based on a time–frequency noise model computed in a quasi-continuous way. Our algorithm makes use of the local bandwidth variability of cardiac electrical representation and splits the discrete time sequence into two sub-planes. The background activities of any origin (muscle, power line interference, etc) are measured in the regions of the time–frequency plane, situated above the local bandwidth of the signal. The noise estimate on each particular scale is non-uniformly sampled and needs to be extrapolated to the regions where the components of cardiac representation are normally expected. On the lower scales, the noise contribution is computed with the use of square polynomial extrapolation. The time–frequency representation of noise, partially measured and partially calculated, is arithmetically subtracted from the noisy signal, and the inverse time–frequency transform yields a noise-free cardiac representation. The algorithm was tested with the use of CSE database records with the addition of MIT-BIH database noise patterns. The static and dynamic performance of the algorithm is sufficient to ameliorate the signal-to-noise ratio by more than 11 dB.
Mid-Infrared Interferometry of Dust around Massive Evolved Stars

We report long-baseline interferometric measurements of circumstellar dust around massive evolved stars with the MIDI instrument on the Very Large Telescope Interferometer and provide spectrally dispersed visibilities in the 8-13 μm wavelength band. We also present diffraction-limited observations at 10.7 μm on the Keck Telescope with baselines up to 8.7 m, which explore larger scale structure. We have resolved the dust shells around the late-type WC stars WR 106 and WR 95 and the enigmatic NaSt 1 (formerly WR 122), suspected to have recently evolved from a luminous blue variable (LBV) stage. For AG Car, the prototypical LBV in our sample, we marginally resolve structure close to the star, distinct from the well-studied detached nebula. The dust shells around the two WC stars show fairly constant size in the 8-13 μm MIDI band, with Gaussian half-widths of ~25 to 40 mas, and the Keck observations reveal an additional extended structure around WR 106. The visibility profiles for NaSt 1 obtained from two MIDI baselines indicate a compact source embedded in an extended structure. The compact dust we detect around NaSt 1 and AG Car favors recent or ongoing dust formation. Using the measured visibilities, we build spherically symmetric radiative transfer models of the WC dust shells, which enable detailed comparison with existing SED-based models. Our results indicate that the inner radii of the shells are within a few tens of AU from the stars. In addition, our models favor grain size distributions with large (~1 μm) dust grains. This proximity of the inner dust to the hot central star emphasizes the difficulty faced by current theories in forming dust in the hostile environment around WR stars. Although we detect no direct evidence for binarity for these objects, dust production in a colliding-wind interface in a binary system is a feasible mechanism in WR systems under these conditions.
Behavior Subtraction

Background subtraction has been a driving engine for many computer vision and video analytics tasks. Although its many variants exist, they all share the underlying assumption that photometric scene properties are either static or exhibit temporal stationarity. While this works in many applications, the model fails when one is interested in discovering changes in scene dynamics instead of changes in scene's photometric properties; the detection of unusual pedestrian or motor traffic patterns are but two examples. We propose a new model and computational framework that assume the dynamics of a scene, not its photometry, to be stationary, i.e., a dynamic background serves as the reference for the dynamics of an observed scene. Central to our approach is the concept of an event, which we define as short-term scene dynamics captured over a time window at a specific spatial location in the camera field of view. Unlike in our earlier work, we compute events by time-aggregating vector object descriptors that can combine multiple features, such as object size, direction of movement, speed, etc. We characterize events probabilistically, but use low-memory, low-complexity surrogates in a practical implementation. Using these surrogates amounts to behavior subtraction, a new algorithm for effective and efficient temporal anomaly detection and localization. Behavior subtraction is resilient to spurious background motion, such as due to camera jitter, and is content-blind, i.e., it works equally well on humans, cars, animals, and other objects in both uncluttered and highly cluttered scenes. Clearly, treating video as a collection of events rather than colored pixels opens new possibilities for video analytics.
Injections of Algesic Solutions into Muscle Activate the Lateral Reticular Formation: A Nociceptive Relay of the Spinoreticulothalamic Tract

Although musculoskeletal pain disorders are common clinically, the central processing of muscle pain is little understood. The present study reports on central neurons activated by injections of algesic solutions into the gastrocnemius muscle of the rat, and their subsequent localization by c-Fos immunohistochemistry in the spinal cord and brainstem. An injection (300μl) of an algesic solution (6% hypertonic saline, pH 4.0 acetate buffer, or 0.05% capsaicin) was made into the gastrocnemius muscle and the distribution of immunolabeled neurons compared to that obtained after control injections of phosphate buffered saline [pH 7.0]. Most labeled neurons in the spinal cord were found in laminae IV-V, VI, VII and X, comparing favorably with other studies, with fewer labeled neurons in laminae I and II. This finding is consistent with the diffuse pain perception due to noxious stimuli to muscles mediated by sensory fibers to deep spinal neurons as compared to more restricted pain localization during noxious stimuli to skin mediated by sensory fibers to superficial laminae. Numerous neurons were immunolabeled in the brainstem, predominantly in the lateral reticular formation (LRF). Labeled neurons were found bilaterally in the caudalmost ventrolateral medulla, where neurons responsive to noxious stimulation of cutaneous and visceral structures lie. Immunolabeled neurons in the LRF continued rostrally and dorsally along the intermediate reticular nucleus in the medulla, including the subnucleus reticularis dorsalis caudally and the parvicellular reticular nucleus more rostrally, and through the pons medial and lateral to the motor trigeminal nucleus, including the subcoerulear network. Immunolabeled neurons, many of them catecholaminergic, were found bilaterally in the nucleus tractus solitarii, the gracile nucleus, the A1 area, the CVLM and RVLM, the superior salivatory nucleus, the nucleus locus coeruleus, the A5 area, and the nucleus raphe magnus in the pons. The external lateral and superior lateral subnuclei of the parabrachial nuclear complex were consistently labeled in experimental data, but they also were labeled in many control cases. The internal lateral subnucleus of the parabrachial complex was labeled moderately. Few immunolabeled neurons were found in the medial reticular formation, however, but the rostroventromedial medulla was labeled consistently. These data are discussed in terms of an interoceptive, multisynaptic spinoreticulothalamic path, with its large receptive fields and role in the motivational-affective components of pain perceptions.
Optimal lengths for DNAs encapsidated by Epstein-Barr virus

We measured the efficiency of DNA packaging by Epstein-Barr virus (EBV) as a function of the length of the DNA being packaged. Plasmids that contain oriP (the origin of latent EBV DNA replication), oriLyt (the origin of lytic EBV DNA replication), the viral terminal repeats (necessary for cleavage and packaging by EBV), and various lengths of bacteriophage lambda DNA were introduced into EBV-positive cells. Upon induction of the resident EBV's lytic phase, introduced plasmids replicated as concatemers and were packaged. Plasmid-derived concatemers of DNA with certain lengths were found to predominate in isolated virion particles. We measured the distribution of lengths of plasmid concatemers found within cells supporting the lytic phase of the viral life cycle and found that this distribution differed from the distribution of lengths of concatemers found in mature virion particles. This finding indicates that the DNA packaged into mature virions represents a selected subset of those present in the cell during packaging. These observations together indicate that the length of DNA affects the efficiency with which that DNA is packaged by EBV. Finally, we measured the length of the packaged B95-8 viral DNA and found it to be approximately 165 kbp, or 10 kbp shorter than the originally predicted size for B95-8 based on its sequence. Together with the results of other studies, these findings indicate that the packaging of DNAs by EBV is dependent on two imprecisely recognized elements: the viral terminal repeats and the length of the DNA being packaged by the virus.