gebhart/patrepeval huggingface dataset:
A Proteomic View of the Cross-Talk Between Early Intestinal Microbiota and Poultry Immune System (2020)

Proteomics has been used to investigate cross-talk between the intestinal microbiome and host biological processes. In this study, an <i>in ovo</i> technique and a proteomics approach was used to address how early bacterial colonization in the gastrointestinal tract (GIT) could modulate inflammatory and immune responses in young broilers. Embryos at 18 embryogenic days were inoculated with saline (S), 10<sup>2</sup> CFU of <i>Citrobacter freundii</i> (CF), <i>Citrobacter</i> species (C2), or lactic acid bacteria mixture (L) into the amnion. At 10 days posthatch, ileum samples from 12 birds per treatment were selected for tandem mass spectrometry analysis. Our further findings indicated that treatment-specific influences on early GIT microbiota resulted in different immune responses in mature broilers. Predicted functional analyses revealed activation of inflammation pathways in broilers treated <i>in ovo</i> with L and CF. Exposure to L enhanced functional annotation related to activation, trafficking of immune cells, and skeletal growth based-network, while CF inhibited biological functions associated with immune cell migration and inflammatory response. These results highlighted that proper immune function was dependent on specific GIT microbiota profiles, in which early-life exposure to L-based probiotic may have modulated the immune functions, whereas neonatal colonization of <i>Enterobacteriaceae</i> strains may have led to immune dysregulation associated with chronic inflammation.
Relationship between breast milk sCD14, TGF‐β1 and total IgA in the first month and development of eczema during infancy (2013)

Levels of breast milk immune parameters were not associated with eczema outcomes or sensitization in infants at 12 months. This suggests that apparent immunological effects on breast milk immunomodulatory factors may not necessarily lead to clinical benefits, and these immune markers may not be critical determinants of allergic disease in infancy.
Genuine Counterfactual Communication with a Nanophotonic Processor (2019)

In counterfactual communication particles and information can travel in opposite directions. With our high-fidelity programmable nanophotonic processor we implement the first trace-free counterfactual protocol without post-selection with a counterfactual violation as low as 2.4%.
ChemInform Abstract: A Formal Synthesis of Crinipellin B Based on the Arene—Alkene meta‐Photocycloaddition Reaction. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Therapy-related acute myeloid leukemia and myelodysplastic syndromes in patients with Hodgkin lymphoma: a report from the German Hodgkin Study Group (2014)

Therapy-related acute myeloid leukemia and myelodysplastic syndromes (t-AML/MDS) represent severe late effects in patients treated for Hodgkin lymphoma (HL). Because more recent data are scarce, we retrospectively analyzed incidence, outcome, and risk factors for the development of t-AML/MDS after HL. A total of 11,952 patients treated for newly diagnosed HL within German Hodgkin Study Group trials between 1993 and 2009 were considered. At a median follow-up of 72 months, t-AML/MDS was diagnosed in 106/11,952 patients (0.9%). Median time from HL treatment to t-AML/MDS was 31 months. The median age of patients with t-AML/MDS was higher than in the whole patient group (43 vs 34 years, P < .0001). Patients who received 4 or more cycles of BEACOPP(escalated) had an increased risk to develop t-AML/MDS when compared with patients treated with less than 4 cycles of BEACOPP(escalated) or no BEACOPP chemotherapy (1.7% vs 0.7% vs 0.3%, P < .0001). The median overall survival (OS) for all t-AML/MDS patients was 7.2 months. However, t-AML/MDS patients proceeding to allogeneic stem cell transplantation had a significantly better outcome with a median OS not reached after a median follow-up of 41 months (P < .001).
Selective Brain Damage: Measuring the Disparate Impact of Model Pruning (2019)

Neural network pruning techniques have demonstrated it is possible to remove
the majority of weights in a network with surprisingly little degradation to
test set accuracy. However, this measure of performance conceals significant
differences in how different classes and images are impacted by pruning. We
find that certain examples, which we term pruning identified exemplars (PIEs),
and classes are systematically more impacted by the introduction of sparsity.
Removing PIE images from the test-set greatly improves top-1 accuracy for both
pruned and non-pruned models. These hard-to-generalize-to images tend to be
mislabelled, of lower image quality, depict multiple objects or require
fine-grained classification. These findings shed light on previously unknown
trade-offs, and suggest that a high degree of caution should be exercised
before pruning is used in sensitive domains.
An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 in human airway epithelial cell cultures and multiple coronaviruses in mice (2020)

Coronaviruses (CoVs) traffic frequently between species resulting in novel disease outbreaks, most recently exemplified by the newly emerged SARS-CoV-2, the causative agent of COVID-19. Herein, we show that the ribonucleoside analog β-D-N4-hydroxycytidine (NHC, EIDD-1931) has broad spectrum antiviral activity against SARS-CoV-2, MERS-CoV, SARS-CoV, and related zoonotic group 2b or 2c Bat-CoVs, as well as increased potency against a coronavirus bearing resistance mutations to the nucleoside analog inhibitor remdesivir. In mice infected with SARS-CoV or MERS-CoV, both prophylactic and therapeutic administration of EIDD-2801, an orally bioavailable NHC-prodrug (β-D-N4-hydroxycytidine-5′-isopropyl ester), improved pulmonary function, and reduced virus titer and body weight loss. Decreased MERS-CoV yields in vitro and in vivo were associated with increased transition mutation frequency in viral but not host cell RNA, supporting a mechanism of lethal mutagenesis in CoV. The potency of NHC/EIDD-2801 against multiple coronaviruses and oral bioavailability highlight its potential utility as an effective antiviral against SARS-CoV-2 and other future zoonotic coronaviruses.
Myoclonus and dystonia in cerebrotendinous xanthomatosis (2012)

These results expand the phenotype of CTX and suggest that myoclonus and/or dystonia are underdiagnosed. In keeping with our findings, tremors previously observed in CTX patients might actually correspond to myoclonic events. We hypothesize that a dysfunction of the dentate nuclei-basal ganglia pathway may be involved.
Sugar Transport in Isolated Corn Root Protoplasts (1984)

Isolated corn (Zea mays L.) root protoplasts were used to study sucrose and hexose uptake. It is found that glucose was preferentially taken up by the protoplasts over sucrose and other hexoses. Glucose uptake showed a biphasic dependence on external glucose concentration with saturable (K(m) of 7 millimolar) and linear components. In contrast, sucrose uptake only showed a linear kinetic curve. Sucrose and glucose uptake were linear over a minimum of 1 hour at pH 6.0 and 1 millimolar exogenous sugar concentration. Glucose uptake showed a sharp 42 degrees C temperature optimum, while sucrose uptake showed a lower temperature sensitivity which did not reach a maximum below 50 degrees C. Uptake of both sugars was sensitive to several metabolic inhibitors and external pH. Differences between sucrose and glucose uptake in two different sink tissue (i.e. protoplasts from corn roots and soybean cotyledons) are discussed.
Wireless Network Evolution: 2G to 3G (2001)

From the Publisher:
3G networks: architecture, planning, migration, management, and optimization. 

Network architectures, planning, management, and optimization
3G air interfaces: UTRA/W-CDMA and cdma2000
3G data services: UTRA/W-CDMA, cdma2000, GPRS, and EDGE
Evolutionary paths for 2G networks
WLL, WAP, and more 


New 3G systems will trigger an explosion in wireless Internet and data applications by delivering far higher data rates than have ever been possible in wireless systems before. In Wireless Network Evolution: 2G to 3G, renowned wireless expert Vijay K. Garg covers key 3G standard and every technical issue associated with planning, management, and optimization of 3G systems. Garg reviews the fundamental principles underlying existing 2G systems, then offers specific, practical guidance on migration to 3G. Coverage includes: 

3G standards activities
3G European and North American systems
3G data services for UTRA/W-CDMA, cdma2000, GPRS, and EDGE networks
Wireless Application Protocol (WAP) and 3G systems
Major 3G enhancements for WLL applications
New RF optimization techniques for 3G systems


Wireless Network Evolution: 2G to 3G will be an invaluable resource for every practicing telecommunications engineer and technical decision maker involved in 3G planning, deployment, or management.
In tight spaces (2011)

We report experiments in which the line shape of the Lyman-alpha (1S-2P) transition was measured for positronium (Ps) atoms both inside and outside a porous silica target. The energy interval E for confined atoms was observed to be larger than that of free Ps by 1:26 AE 0:06 meV. A configuration interaction calculation yields results that are consistent with our $5 nm sample, and suggests that E decreases dramatically for larger cavity diameters. The linewidth of the transition, 0:066 AE 0:004 nm (FWHM), is about half of what one would expect for free Ps at room temperature due to the Dicke line narrowing effect of confinement. Such measurements can be used to determine void sizes in porous films and Ps dynamics therein, and elimination of the Doppler spread of atoms in a porous film could be useful for the efficient excitation of a Ps gas.
Supplemental legend from Phase I Study of Single-Agent Utomilumab (PF-05082566), a 4-1BB/CD137 Agonist, in Patients with Advanced Cancer (2023)

&lt;p&gt;Supplemental legend&lt;/p&gt;
Flavors and Fragrances, 4. Natural Raw Materials (2015)

The article contains sections titled: 1. Introduction 2. Isolation of Natural Fragrance and Flavor Concentrates 2.1. Essential Oils 2.2. Extracts 3. Survey of Natural Raw Materials
Structural and functional characterization of CFE88: Evidence that a conserved and essential bacterial protein is a methyltransferase (2005)

CFE88 is a conserved essential gene product from Streptococcus pneumoniae. This 227-residue protein has minimal sequence similarity to proteins of known 3D structure. Sequence alignment models and computational protein threading studies suggest that CFE88 is a methyltransferase. Characterization of the conformation and function of CFE88 has been performed by using several techniques. Backbone atom and limited side-chain atom NMR resonance assignments have been obtained. The data indicate that CFE88 has two domains: an N-terminal domain with 163 residues and a C-terminal domain with 64 residues. The C-terminal domain is primarily helical, while the N-terminal domain has a mixed helical/extended (Rossmann) fold. By aligning the experimentally observed elements of secondary structure, an initial unrefined model of CFE88 has been constructed based on the X-ray structure of ErmC' methyltransferase (Protein Data Bank entry 1QAN). NMR and biophysical studies demonstrate binding of S-adenosyl-L-homocysteine (SAH) to CFE88; these interactions have been localized by NMR to the predicted active site in the N-terminal domain. Mutants that target this predicted active site (H26W, E46R, and E46W) have been constructed and characterized. Overall, our results both indicate that CFE88 is a methyltransferase and further suggest that the methyltransferase activity is essential for bacterial survival.
Restoration of astronomical images by an iterative superresolution algorithm (2003)

In this work a new fast method for super-resolving noisy images is described. The iterative technique is similar to the positive constraint algorithm but faster and more effective in terms of the resulting global noise in the image. The astronomical use of the technique is illustrated by applying it to the LMC 49-50 (04/01/98) image. Results from this method are compared with those of well-known algorithms such as the Wiener filter, the positive constraint, the maximum a posteriori probability, and the Lucy-Richardson method.
Millimeter Wave Wireless-Assisted Robotic Navigation with Link State Classification. (2021)

The millimeter wave (mmWave) bands have attracted considerable attention for high precision localization applications due to the ability to capture high angular and temporal resolution measurements. This paper explores mmWave-based positioning for a target localization problem where a fixed target broadcasts mmWave signals and a mobile robotic agent attempts to listen to the signals to locate and navigate to the target. A three strage procedure is proposed: First, the mobile agent uses tensor decomposition methods to detect the wireless paths and their angles. Second, a machine-learning trained classifier is then used to predict the link state, meaning if the strongest path is line-of-sight (LOS) or non-LOS (NLOS). For the NLOS case, the link state predictor also determines if the strongest path arrived via one or more reflections. Third, based on the link state, the agent either follows the estimated angles or explores the environment. The method is demonstrated on a large dataset of indoor environments supplemented with ray tracing to simulate the wireless propagation. The path estimation and link state classification are also integrated into a state-ofthe-art neural simultaneous localization and mapping (SLAM) module to augment camera and LIDAR-based navigation. It is shown that the link state classifier can successfully generalize to completely new environments outside the training set. In addition, the neural-SLAM module with the wireless path estimation and link state classifier provides rapid navigation to the target, close to a baseline that knows the target location.
Embodying Physics-Aware Avatars in Virtual Reality (2023)

Embodiment toward an avatar in virtual reality (VR) is generally stronger when there is a high degree of alignment between the user’s and self-avatar’s motion. However, one-to-one mapping between the two is not always ideal when user interacts with the virtual environment. On these occasions, the user input often leads to unnatural behavior without physical realism (e.g., objects penetrating virtual body, body unmoved by hitting stimuli). We investigate how adding physics correction to self-avatar motion impacts embodiment. Physics-aware self-avatar preserves the physical meaning of the movement but introduces discrepancies between the user’s and self-avatar’s motion, whose contingency is a determining factor for embodiment. To understand its impact, we conducted an in-lab study (n = 20) where participants interacted with obstacles on their upper bodies in VR with and without physics correction. Our results showed that, rather than compromising embodiment level, physics-responsive self-avatar improved embodiment compared to no-physics condition in both active and passive interactions.
358 IMAGING AND QUANTIFICATIONS OF BRAIN IRON BASED ON MAGNETIC RESONANCE SUSCEPTIBILITY (2005)

<h3>Purpose</h3> Non-invasive (MRI) attempts to map and quantitate brain iron have been frustrated by the limitations of conventional T1, T2, and proton density imaging. Since the relationship of brain iron accumulation to the pathogenesis of a number of neurodegenerative diseases (AD = Alzheimer9s Disease, PD = Parkinson9s Disease) is a matter of current interest, investigating new MR imaging technology is warranted. Susceptibility weighted MR imaging (SWI) has been applied in this study to both a mouse brain model and elderly humans at risk for AD. <h3>Methods</h3> 85 humans (54 MCI and 29 control) have had initial SWI studies and 22 have had repeated MRIs. This imaging was conducted on a 1.5T Siemens Vision System and collected data from 10 regions (motor and cingulate cortex, thalamus, hippocampus, putamen, red nuclei, substantial nigra, substantia inominata, globus pallidus, and caudate nucleus). Collected data was analyzed for iron deposits with the Spin Echo/Gradient Method. <h3>Results</h3> Processed data is available in 24 cases with initial SWI images (10 mild cognitive impairment (MCI), 14 control), 11 cases (5 MCI, 6 control) have had follow-up scans at one year. The SWI imaging technique enables a quantitation differentiation of grey, white matter, and CSF. Though our findings remain provisional, there is only a small number of conversions from MCI to AD noted in repeat studies. This suggests a trend of enhanced iron accumulation in the red nucleus of an MCI case that converted to AD. <h3>Conclusions</h3> This study represents the first direct correlations of a novel MR imaging technique with direct measurement of brain iron in its various forms (total, loosely bound, non-heme Fe) with extrapolation to humans. We have established that the sensitivity of the technique enables a description of phase variation for the red nuclei as an example that follow Gaussian Statistics with standard devices of about 30 units and with means for gray matter (1785 to 1855). CSF is 2075 to 2165. Any deviation about 3 S.D.9s is being considered as significant. SWI imaging proves a novel, sensitive, and apparently specific technology for the imaging and quantification of brain iron. The baseline for the study has been established and will develop with clinical follow-up over the next 3 years.
Strategies for the molecular genetic analysis of obesity in humans (1993)

Studies of twins, adopted children, and some human populations indicate that body composition is significantly influenced by genetic factors. However, in no specific instance in either man or animals is the precise etiology of obesity known at the molecular level. Attempts to identify the molecular basis of obesity in humans have been hampered by difficulties in measuring food intake and energy expenditure with sufficient accuracy, as well as the apparent polygenic control of body composition in man. These constraints have stimulated interest in inbred animal strains, particularly mice, that have a genetic predisposition to obesity. Using the techniques of positional cloning, molecular markers flanking two autosomal recessive mouse obesity mutants (ob and db), which demonstrate a metabolic/behavioral phenotype similar to that observed in obese humans, have been identified. These markers are being used: (1) as starting points for chromosome walks to identify these genes, (2) as an aid in identifying genetically obese rodents prior to the development of the experimentally confounding obese phenotype, and (3) to investigate the possible contribution of the ob and db gene products to obesity in families segregating an obese phenotype. Additionally, genetic crosses segregating these obesity mutations are being used to identify "polygenes" that influence the severity of obesity and type II diabetes. Such studies may ultimately lead to the characterization of genes that influence the development and severity of obesity and non-insulin-dependent diabetes (NIDDM) in humans.
The suppression of immune activation during enfuvirtide-based salvage therapy is associated with reduced CCR5 expression and decreased concentrations of circulating interleukin-12 and IP-10 during 48 weeks of longitudinal follow-up (2010)

This study shows that suppression of HIV-1 replication with enfuvirtide-based salvage therapy in patients with low CD4 cell counts may result in an immunological benefit, characterized by the restoration of CD4 T-cell subsets associated with decreased immune activation and suppression of inflammation.
Understanding the Active Sites of CO Hydrogenation on Pt–Co Catalysts Prepared Using Atomic Layer Deposition (2017)

The production of liquid fuels and industrial feedstocks from renewable carbon sources is an ongoing scientific challenge. Using atomic layer deposition together with conventional techniques, we synthesize Pt–Co bimetallic catalysts that show improvement for syngas conversion to alcohols. By combining reaction testing, X-ray diffraction, electron microscopy, and in situ infrared spectroscopy experiments, supported by density functional theory calculations, we uncover insights into how Pt modulates the selectivity of Co catalysts. The prepared Pt–Co catalysts demonstrate increased selectivity toward methanol and low molecular weight hydrocarbons as well as a modest increase in selectivity toward higher alcohols. The in situ infrared spectroscopic measurements suggest that these changes in selectivity result from an interplay between linear and bridging carbon monoxide configurations on the catalyst surface.
Analysis of six hundred and twenty-two intertrochanteric hip fractures. (1979)

Of 622 intertrochanteric fractures, 57% were stable (Types I and II). Twenty-eight per cent were Type III, and 15% were Type IV (the unstable types). The 150-degree telescoping Massie nail proved superior to the fixed 135-degree Jewett nail (particularly for unstable fractures) because it allowed a controlled impaction of the fracture fragments to a stable position. In about one-third of the fractures, some medial displacement occurred. With anatomical reduction and the use of the Massie or ASIF nails, we achieved a decrease in the morbidity and mortality and 96% satisfactory results. Our prospective study was compared with a retrospective study in which other devices were used. Early ambulation and weight-bearing also was a major contributing factor to the improved results in the prospective study. Intertrochanteric hip fractures that are unstable can be fixed with a collapsible nail, and that treatment appears to give as good or better results than the displacement method of Dimon and Hughston or Sarmiento.
Probing a Gas/Liquid Acid–Base Reaction by X‐ray Photoelectron Spectroscopy (2013)

A mechanistic study: In a Brønsted acid/base reaction, gaseous triflic acid (OTfH) transfers its proton to the basic Cl− anion of the ionic liquid [C8C1Im]Cl forming volatile HCl and the IL [C8C1Im][TfO]. This anion exchange reaction is monitored in the near-surface region quantitatively by X-ray photoelectron spectroscopy as a function of time (see picture; BE=binding energy). As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.