Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of varying dietary starch and fiber levels and inoculum source (mule deer vs. dairy cow) on simulated rumen fermentation characteristics.

This study measured starch and fiber digestion and microbial fermentation of three commercial exotic animal feeds using mule deer (MD) or dairy cow (DC) rumen inoculum. Diets were formulated to provide either high starch/low fiber (based on neutral detergent fiber fraction; NDF) with either alfalfa (diet A) or grain and oilseed byproducts (diet B) as the major fiber sources or low starch/high NDF (diet C). An initial batch culture incubation was run with diets inoculated with each rumen inoculum (n = 6; N = 36) over a 48 hr period with samples taken at different hour points for ammonia, pH, lactate, and volatile fatty acids (VFA). A second experiment was conducted where two continuous culture incubations (MD or DC) were run with six single-flow polycarbonate fermentation vessels per dietary treatment. Diets were fed two times a day over an 8-day period and sampled for ammonia, pH, and VFA before and after feeding on the last 3 days. On day 8, fermenter and effluent contents were collected and analyzed for nitrogen, dry matter digestibility (DMD), and organic matter digestibility (OMD). OMD was greater in MD (P = 0.02) and DMD tended to do the same (P = 0.06), but there were no differences due to diet (P > 0.05). Ammonia concentration was greater in DC (P < 0.01), and diets A and B had greater concentrations than diet C (P < 0.01). The greater digestibility, higher acetate:propionate (A:P) ratio and increased lactate levels prior to feeding likely led to diet C having a lower pH than diet A (6.59 vs. 6.66, respectively; P < 0.01) and led the tendency of A to be lower than C after feeding (P = 0.08). A:P ratio was greater in DC than MD before and after feeding (P < 0.01) and was greater in diet C than diets A or B (P < 0.01). Total VFA production tended to be greater in diets B and C in DC (P = 0.06). Rumen fluid source did affect fermentation. Increasing fiber level did not negatively affect fermentation and may increase OMD by removal of negative associative affects by starch on cellulolytic bacteria.
Extensive remodeling of a cyanobacterial photosynthetic apparatus in far-red light

Making sure leftover light gets in Bacteria that harvest sunlight through photosynthesis are everywhere and are vital for absorbing carbon dioxide. Like plants in a jungle, these cells have to compete for access to light. Gan et al. found that one species of such cyanobacteria, Leptolyngbya, survives on the scraps of leftover light that other photosynthetic cells can't use. When the light is crowded out by competing organisms, Leptolyngbya changes the pathways in its cells that make the light-harvesting molecules and remodels them into structures that can use redder light at longer wavelengths that is unused by other cells. Science, this issue p. 1312 Light harvesting in a mat-forming bacterium is biosynthetically optimized, even at extreme wavelengths. Cyanobacteria are unique among bacteria in performing oxygenic photosynthesis, often together with nitrogen fixation and, thus, are major primary producers in many ecosystems. The cyanobacterium, Leptolyngbya sp. strain JSC-1, exhibits an extensive photoacclimative response to growth in far-red light that includes the synthesis of chlorophylls d and f. During far-red acclimation, transcript levels increase more than twofold for ~900 genes and decrease by more than half for ~2000 genes. Core subunits of photosystem I, photosystem II, and phycobilisomes are replaced by proteins encoded in a 21-gene cluster that includes a knotless red/far-red phytochrome and two response regulators. This acclimative response enhances light harvesting for wavelengths complementary to the growth light (λ = 700 to 750 nanometers) and enhances oxygen evolution in far-red light.
On representations by low-degree polynomials

In the first part of the paper we show that a subset S of a boolean cube B/sub n/ embedded in the projective space P/sup n/ can be approximated by a subset of B/sub n/ defined by nonzeroes of a low-degree polynomial only if the values of the Hilbert function of S are sufficiently small relative to the size of S. The use of this property provides a simple and direct technique for proving lower bounds on the size of ACC[p/sup r/] circuits. In the second part we look at the problem of computing many-output function by ACC[p/sup r/] circuit and give an example when such a circuit can be correct only at exponentially small fraction of assignments. <<ETX>>
Investigation of the in vitro photocatalytic antibacterial activity of nanocrystalline TiO2 and coupled TiO2/Ag containing copolymer on the surface of medical grade titanium

Antibacterial surfaces have been in the focus of research for years, driven by an unmet clinical need to manage an increasing incidence of implant-associated infections. The use of silver has become a topic of interest because of its proven broad-spectrum antibacterial activity and track record as a coating agent of soft tissue implants and catheters. However, for the time being, the translation of these technological achievements for the improvement of the antibacterial property of hard tissue titanium (Ti) implants remains unsolved. In our study, we focused on the investigation of the photocatalysis mediated antibacterial activity of silver (Ag), and Ti nanoparticles instead of their pharmacological effects. We found that the photosensitisation of commercially pure titanium discs by coating them with an acrylate-based copolymer that embeds coupled Ag/Ti nanoparticles can initiate the photocatalytic decomposition of adsorbed S. salivarius after the irradiation with an ordinary visible light source. The clinical isolate of S. salivarius was characterised with MALDI-TOF mass spectrometer, while the multiplication of the bacteria on the surface of the discs was followed-up by MTT assay. Concerning practical relevance, the infected implant surfaces can be made accessible and irradiated by dental curing units with LED and plasma arc light sources, our research suggests that photocatalytic copolymer coating films may offer a promising solution for the improvement of the antibacterial properties of dental implants.
A local macrophage chemokine network sustains protective tissue-resident memory CD4 T cells

Resident memory T cells sound the alarm Immunological memory protects against reinfection. Resident memory T cells (TRM) are long-lived and remain in the tissues where they first encountered a pathogen (see the Perspective by Carbone and Gebhardt). Schenkel et al. and Ariotti et al. found that CD8+ TRM cells act like first responders in the female reproductive tissue or the skin of mice upon antigen reencounter. By secreting inflammatory proteins, TRM cells rapidly activated local immune cells to respond, so much so that they protected against infection with an unrelated pathogen. Iijima and Iwasaki found that CD4+ TRM cells protected mice against reinfection with intravaginal herpes simplex virus 2. Science, this issue p. 98, p. 101, p. 93; see also p. 40 Tissue-resident memory CD4+ T cells protect mice against lethal reinfection with herpes simplex virus 2. [Also see Perspective by Carbone and Gebhardt] CD8 tissue-resident memory T (TRM) cells provide efficient local control of viral infection, but the role of CD4 TRM is less clear. Here, by using parabiotic mice, we show that a preexisting pool of CD4 TRM cells in the genital mucosa was required for full protection from a lethal herpes simplex virus 2 (HSV-2) infection. Chemokines secreted by a local network of macrophages maintained vaginal CD4 TRM in memory lymphocyte clusters (MLCs), independently of circulating memory T cells. CD4 TRM cells within the MLCs were enriched in clones that expanded in response to HSV-2. Our results highlight the need for vaccine strategies that enable establishment of TRM cells for protection from a sexually transmitted virus and provide insights as to how such a pool might be established.
Hepatitis C can be cured globally, but at what cost?

New drugs to cure hepatitis C should be made available at low costs in developing countries Worldwide, an estimated 185 million people have been infected with the hepatitis C virus (HCV). Untreated, the infection can lead to cirrhosis, liver failure, and liver cancer, causing up to 500,000 related deaths per year (1, 2), and killing more people than tuberculosis or malaria (3, 4). New treatments are available that can cure over 90% of people with HCV within 12 weeks (5). So what is the problem?
Coping with the curse of freshwater variability

Institutions, infrastructure, and information for adaptation Coping with variable and unpredictable freshwater resources represents a profound challenge to climate adaptation. Rainfall, snowmelt, soil moisture, and runoff can vary from zero to large quantities, over a range of time scales and in ways not well predicted by climate models. Extreme floods and droughts are the most obvious manifestations, but hydrologic variability can also have chronic impacts. Water security involves managing these risks so that they do not place an intolerable burden on society and the economy (1). We discuss interlinked roles of institutions, infrastructure, and information in managing those risks.
Commensal microbes and interferon-λ determine persistence of enteric murine norovirus infection

Turning viral persistence on and off Norovirus causes >90% of the world's gastroenteritis. Norovirus can establish persistent infections, which may contribute to its spread. How does norovirus establish itself as a permanentw resident of the gut and how can such persistent infections be cured (see the Perspective by Wilks and Golovkina)? Baldridge et al. studied mice persistently infected with norovirus and found that viral persistence required the gut microbiota: resident bacteria in the gastrointestinal tract. Antibiotics prevented persistent mouse norovirus infection in a way that depended on the secreted antiviral protein interferon λ (IFN-λ). Nice et al. report that IFN-λ can cure mice persistently infected with norovirus, independent of the adaptive immune system. Science, this issue p. 266, p. 269; see also p. 233 Persistent norovirus infection in mice requires the gut microbiota. [Also see Perspective by Wilks and Golovkina] The capacity of human norovirus (NoV), which causes >90% of global epidemic nonbacterial gastroenteritis, to infect a subset of people persistently may contribute to its spread. How such enteric viruses establish persistent infections is not well understood. We found that antibiotics prevented persistent murine norovirus (MNoV) infection, an effect that was reversed by replenishment of the bacterial microbiota. Antibiotics did not prevent tissue infection or affect systemic viral replication but acted specifically in the intestine. The receptor for the antiviral cytokine interferon-λ, Ifnlr1, as well as the transcription factors Stat1 and Irf3, were required for antibiotics to prevent viral persistence. Thus, the bacterial microbiome fosters enteric viral persistence in a manner counteracted by specific components of the innate immune system.
Structural basis for microRNA targeting

Repressing the right (and not the wrong) mRNA MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression by targeting a repressor complex to specific messenger RNAs (mRNAs). Schirle et al. determined structures of a miRNA bound to both the central component of the repressor complex, the protein Argonaute-2 (Ago2), and a target mRNA (see the Perspective by Patel). The miRNA in the complex first recognizes a short region of complementary sequence in the mRNA. This initial interaction promotes structural changes that allow the complex to bind additional target sequences. The authors suggest that in the absence of extensive miRNA-mRNA pairing, the repressor complex active site is rendered inactive, preventing repression of nontarget mRNAs. Science, this issue p. 608; see also p. 542 Structures of microRNA bound to the Ago2 repressor protein and messenger RNA elucidate target specificity. [Also see Perspective by Patel] MicroRNAs (miRNAs) control expression of thousands of genes in plants and animals. miRNAs function by guiding Argonaute proteins to complementary sites in messenger RNAs (mRNAs) targeted for repression. We determined crystal structures of human Argonaute-2 (Ago2) bound to a defined guide RNA with and without target RNAs representing miRNA recognition sites. These structures suggest a stepwise mechanism, in which Ago2 primarily exposes guide nucleotides (nt) 2 to 5 for initial target pairing. Pairing to nt 2 to 5 promotes conformational changes that expose nt 2 to 8 and 13 to 16 for further target recognition. Interactions with the guide-target minor groove allow Ago2 to interrogate target RNAs in a sequence-independent manner, whereas an adenosine binding-pocket opposite guide nt 1 further facilitates target recognition. Spurious slicing of miRNA targets is avoided through an inhibitory coordination of one catalytic magnesium ion. These results explain the conserved nucleotide-pairing patterns in animal miRNA target sites first observed over two decades ago.
Gellan gum macrobeads loaded with naproxen: The impact of various naturally derived polymers on pH-dependent behavior

Aims After oral administration, naproxen generates several side-effects related to stomach malfunction. Undoubtedly, the enteric dosage forms with naproxen can be considered as safer. Moreover, since it has been evidenced that development and growth of colorectal cancer is related to the presence of cyclooxygenase, naproxen is investigated in terms of the tumor prevention. The aim of the present work was to formulate and evaluate the properties of novel naproxen-loaded macrobeads, made on the basis of low-acyl gellan gum and its blends with carrageenans, guar gum, cellulose sulfate, and dextran sulfates. Method Seven formulations were prepared by ionotropic gelation. The morphology of the dried beads was evaluated by scanning electron microscopy. The next step focused on Raman spectroscopy and thermal analysis of naproxen, polymers, and the beads. Next, the swelling behavior was examined in three acceptor fluids at pH = 1.2; 4.5, and 7.4. The beads were evaluated regarding naproxen content and encapsulation efficiency. The last stage of the work concerned the drug release studies. Results Addition of any other polysaccharide than gellan resulted in flattening of the beads upon drying. Differential scanning calorimetry confirmed the crystalline form of naproxen. Raman spectra showed that no apparent interactions occurred. In the acidic environment, all the beads revealed the tendency to absorb water. The beads swelled to the greatest extent at pH = 4.5. Naproxen was released from the beads at a varied rate. At pH = 7.4, the most prolonged release was observed for the beads containing carrageenans. Conclusions We have proved that blending of gellan with various polysaccharides can change the pH-dependent properties of the beads loaded with naproxen. We believe that the information enclosed in the paper will be of particular importance regarding the development and characteristics of novel oral dosage forms based on natural polymers.
Familial Associations between Cancer Sites

The Utah Population Database links together genealogical records, the Utah Cancer Registry, and Utah death certificates and allows identification of cancer clusters. Groups of individuals with cancers of some types tend to fall into related clusters within the genealogy. We examine the apparent tendency of cases of two types of cancer to cluster together and distinguish real clusters from chance occurrences. Some established associations are found, whereas some are surprisingly absent. Some new associations are also suggested.
Riboswitch regulates RNA

Nutrient metabolism in bacteria is controlled by a circuit in which RNA is regulated by RNA [Also see Reports by DebRoy et al. and Mellin et al.] Bacteria are expert at adapting to various ecological niches, including the human gut, amid multiple other competing organisms. Their success in these many environments means that they have perfected the ability to use what is available, to not waste resources making RNA and protein for unnecessary processes, and to sense and respond when conditions and requirements change. It has become increasingly clear that RNA-based regulation plays an important part in empowering bacteria to respond to environmental changes. On pages 937 and 940 of this issue, DebRoy et al. (1) and Mellin et al. (2), respectively, report a new example of adaptation in which type of RNA-based regulation is controlled by another, allowing the integrated sensing of two different nutrients. The finding points to an unexpected role for riboswitches, RNA binding proteins, and noncoding RNAs in controlling gene expression by joining forces.
Curve and Surface Generation and Refinement Based on a High Speed Derivative Algorithm

Abstract We propose an efficient algorithm for the refinement of curves and surfaces using simple knot B-splines. We develop a high speed algorithm for the computation of the r th derivative of an r th order spline and demonstrate that the inverse of this algorithm leads to an efficient refinement algorithm which is an order of magnitude faster than the well known Oslo algorithm. We show how the high speed derivative algorithm can also be used to directly generate spline curves and surfaces much more efficiently than linear combination algorithms and forward differencing.
On the Use of Calibration for Pedestrian Detection in On-Board Vehicular Cameras

This paper presents a new approach for pedestrian detection in the context of Driver Assistance Systems (DAS). Given a camera with known intrinsic parameters, a flexible online calibration scheme that explores the expected road geometry is used to obtain the extrinsic parameters. With the full camera parameters, the expected geometry and size of a standing person is used to customize a baseline pedestrian detector based on sliding windows and multiple scales. Our experimental results show that the proposed approach allows the use of detachable cameras in the context of DAS, improving the accuracy of the baseline pedestrian detector. Furthermore, the flexible calibration scheme allows to estimate the distance from detected pedestrians to the camera using detachable cameras, opposed to the fixed onboard cameras in commercial vehicles that support vision-based DAS.
A shed NKG2D ligand that promotes natural killer cell activation and tumor rejection

Immune cells, including natural killer (NK) cells, recognize transformed cells and eliminate them in a process termed immunosurveillance. It is thought that tumor cells evade immunosurveillance by shedding membrane ligands that bind to the NKG2D-activating receptor on NK cells and/or T cells, and desensitize these cells. In contrast, we show that in mice, a shed form of MULT1, a high-affinity NKG2D ligand, causes NK cell activation and tumor rejection. Recombinant soluble MULT1 stimulated tumor rejection in mice. Soluble MULT1 functions, at least in part, by competitively reversing a global desensitization of NK cells imposed by engagement of membrane NKG2D ligands on tumor-associated cells, such as myeloid cells. The results overturn conventional wisdom that soluble ligands are always inhibitory and suggest a new approach for cancer immunotherapy. Soluble proteins shed by tumors stimulate natural killer cell–mediated antitumor immunity in mice. [Also see Perspective by Steinle and Cerwenka] Natural born killers for tumors Cancer immunotherapies work by activating cytotoxic lymphocytes, usually CD8+ T cells, to kill tumors. But adding new approaches to the arsenal might boost these therapies. Deng et al. now report that natural killer (NK) cells, another type of lymphocyte, can also kill tumors (see the Perspective by Steinle and Cerwenka). Mouse tumors secrete a protein called MULT1 that binds to a protein called NKG2D on the surface of NK cells. This activates NK cells and signals them to kill the tumor cells. Treating tumorbearing mice with soluble MULT1 caused their NK cells to reject the tumors. Science, this issue p. 136; see also p. 45
Ranking Principal Components in Face Spaces through AdaBoost.M2 Linear Ensemble

Despite the success of Principal Component Analysis (PCA) for dimensionality reduction, it is known that its most expressive components do not necessarily represent important discriminant features for pattern recognition. In this paper, the problem of ranking PCA components, computed from multi-class databases, is addressed by building multiple linear learners that are combined through the AdaBoost.M2 in order to determine the discriminant contribution of each PCA feature. In our implementation, each learner is a weakened version of a linear support vector machine (SVM). The strong learner built by the ensemble technique is processed following a strategy to get the global discriminant vector to sort PCA components according to their relevance for classification tasks. Also, we show how the proposed methodology to compute the global discriminant vector can be applied to other multi-class approaches, like the linear discriminant analysis (LDA). In the computational experiments we compare the obtained approaches with counterpart ones using facial expression experiments. Our experimental results have shown that the principal components selected by the proposed technique allows higher recognition rates using less linear features.
Prevention of Chemotherapy Medication Errors

Prevention of medication errors has long been a concern of pharmacists in all practice settings, including specialty treatment and research centers. Oncology pharmacists have always been particularly aware of this concern because many of the cytotoxic drug therapy regimens we use are already at the maximum tolerated doses, thus leaving no margin for error. During the past 10 years, catastrophic chemotherapy medication errors have occurred in some of the finest hospitals and cancer centers in the United States, bringing unprecedented public and governmental awareness of the risk of such errors. In addition, the March 2000 report by the Institute of Medicine of the National Academy of Sciences, To Err Is Human: Building a Safer Health System, has prompted legislative and executive branch reaction at the federal level aimed toward reducing medical errors of all types, including medication errors. The purpose of this article is to review the types and causes of catastrophic chemotherapy medication errors that have occurred in oncology and to discuss tools and methods aimed at improving the safety of medication use, particularly chemotherapy, in the United States.
Relevance weighting for combining multi-domain data for n-gram language modeling

Standard statistical language modeling techniques suffer from sparse-data problems in tasks where large amounts of domain-specific text are not available. In this paper, we focus on improving the estimation of domain-dependent n -gram models by the selective use of out-of-domain text data. Previous approaches for estimating language models from multi-domain data have not accounted for the characteristic variations of style and content across domains. In contrast, this work aims at differentially weighting subsets of the out-of-domain data according to style and/or content similarity to the given task, where “style" is represented by part-of-speech statistics and “content" by the particular choice of vocabulary items. In addition to n -gram estimation, the differential weights can be used for lexicon design. Recognition experiments are based on the Switchboard corpus of spontaneous conversations, with out-of-domain text drawn from the Wall Street Journal and Broadcast News corpora. The similarity weighting approach gives a 3? 5% reduction in word error rate over a domain-specific n -gram language model, providing some of the largest language modeling gains reported for the Switchboard task in recent years.