Miracle-dz/UniFAR-FTUs huggingface dataset:
Tuning biphenyl dioxygenase for extended substrate specificity.

Highly substituted polychlorinated biphenyls (PCBs) are known to be very resistant to aerobic biodegradation, particularly the initial attack by biphenyl dioxygenase. Functional evolution of the substrate specificity of biphenyl dioxygenase was demonstrated by DNA shuffling and staggered extension process (StEP) of the bphA gene coding for the large subunit of biphenyl dioxygenase. Several variants with an extended substrate range for PCBs were selected. In contrast to the parental biphenyl dioxygenases from Burkholderia cepacia LB400 and Pseudomonas pseudoalcaligenes KF707, which preferentially recognize either ortho- (LB400) or para- (KF707) substituted PCBs, several variants degraded both congeners to about the same extent. These variants also exhibited superior degradation capabilities toward several tetra- and pentachlorinated PCBs as well as commercial PCB mixtures, such as Aroclor 1242 or Aroclor 1254. Sequence analysis confirmed that most variants contained at least four to six template switches. All desired variants contained the Thr335Ala and Phe336Ile substitutions confirming the importance of this critical region in substrate specificity. These results suggest that the block-exchange nature of gene shuffling between a diverse class of dioxygenases may be the most useful approach for breeding novel dioxygenases for PCB degradation in the desired direction.
Massive dualities in six dimensions

We study compactifications of string theory and M-theory to six dimensions with background fluxes. The non-zero fluxes lead to additional mass parameters. We derive the S- and T-duality rules for the corresponding (massive) supergravity theories. Specifically, we investigate the massive T-duality between Type IIA superstring theory compactified on K3 with background fluxes and Type IIB superstring theory compactified on K3. Furthermore, we generalize to the massive case the 6D ‘string–string’ S-duality between M-theory on K3 × S1 and the heterotic string on T4. Whereas in the case of massive T-duality the mass parameters are in the fundamental representation of the U-duality group O(4, 20) we find that in the case of massive S-duality they are in the 3-index antisymmetric representation. In the latter case, the mass parameters involved extend those of Kaloper and Myers. We apply our duality rules to massive brane solutions, such as the domain wall solutions corresponding to the mass parameters and find new massive brane solutions. Finally, we discuss the higher dimensional interpretation of the dualities and brane solutions.
ELEVEN Seed dispersal of woody plants in tropical forests : concepts , examples and future directions

Introduction Understanding seed dispersal is critical to understanding plant population and community dynamics (Nathan & Muller-Landau 2000), especially in tropical forests where seed rain of virtually all plant species is sparse and patchy (Hubbell et al. 1999; Muller-Landau et al. 2002). Seed rain determines potential population growth rates and spatial patterns, as well as the relative influences of postdispersal processes such as seed prédation (e.g. Wright et al. 2000), microhabitat requirements for establishment (e.g. Svenning 1999) and density-dependent survival (e.g. Harms et al. 2000). Despite its importance, we know very little about seed dispersal of tropical trees, because it has been studied in only a tiny proportion of the many tropical tree species and seed dispersers, and because the patterns that have been observed have largely eluded easy generalization. Just as there is a greater diversity of plant species and animal species in the tropics than in other regions, there is also a greater diversity of seed-dispersal strategies and patterns. Seed dispersal by animals predominates it is the main strategy of 70%-90% of tropical forest plant species (Willson et al. 1989) and involves a tremendous diversity of animal species and behaviours. Birds, bats, arboreal and terrestrial mammals (everything from mice to elephants), ants, dung beetles, even ñsh can disperse seeds (Levey et al. 1994). Animals may consume fruit and drop, spit or defecate the seeds, carry seeds in their coats or scatter-hoard seeds for later consumption. Abiotic strategies such as vwnd, water and ballistic dispersal form the main mode of seed movement for the remaining 10%-30% of tropical tree species (Willson et al. 1989). The seeds of many species may experience both primary dispersal (movement before the seed reaches the ground) and secondary dispersal (subsequent movement) usually by different modes or different animal species (e.g. movement by ballistic dispersal and then
Quality improvement in the developing world.

A Quality Improvement (QI) team in a small clinic assessed children’s compliance with a standard treatment plan for a common infectious disease. Compliance was poor. Studying why, the staff discovered that the bad taste of the medicine was a principal problem. Working with mothers, the QI team identified popular foods that could be used to conceal the taste, and they placed in the waiting area a poster showing how to use the foods to do it. In the next test cycle, compliance with the treatment protocol had risen from 48% to 70%. The story is familiar—a successful quality improvement project—but the setting is not. The project team was not in a wealthy American health maintenance organization or a primary care practice in Sweden. In was in a remote African village, the disease was malaria, and the drug was chloroquine [1]. In conjunction with this issue, the International Journal of Quality in Health Care will publish a supplement entitled ‘Quality Assurance in Low- and Middle-Income Countries’. The papers in this supplement are based on the work of the Quality Assurance Project of The United States Agency for International Development (USAID), now in its third 5-year funding cycle. These reports from developing countries are good news both for the field of QI and for the many individuals working to improve health and health care systems in countries with very limited resources. This project has a technical support center in the United States, which provides assistance to developing countries that request it and compete successfully for funds from the local USAID mission. Readers who would like a preview of the supplement can sample the impressive collection of monographs, case studies, and research reports available on the project website [2]. The supplement includes …
A1 mode Lamb wave on thin LiTaO3 for high frequency acoustic devices

The Lamb waves and horizontal shear waves' propagation in LiTaO<sub>3</sub> thin plate is investigated as a function of Euler angles. Both velocity and electromechanical coupling factor largely depend on the plate's thickness. Around (0°, 30°, 0°), LiTaO<sub>3</sub> thin plate has a high velocity and a suitable coupling factor for a high frequency filter. Authors fabricated A<sub>1</sub> mode Lamb wave resonators in (0°, 39°, 0°) LiTaO<sub>3</sub>'s thin plate. Lamb waves' velocities and leaky Lamb wave' velocities were measured by network analyzer and ultrasonic microscopy. Measured velocities correspond to the ones calculated by FEM. Velocities higher than 20,000 m/s were obtained. It is then shown that A<sub>1</sub> mode Lamb wave close to (0°, 30°, 0°) LiTaO<sub>3</sub> thin plate is suitable for high frequency devices.
The NMDA receptor functions independently and as an LRP1 co-receptor to promote Schwann cell survival and migration

ABSTRACT NMDA receptors (NMDA-Rs) are ionotropic glutamate receptors, which associate with LDL-receptor-related protein-1 (LRP1) to trigger cell signaling in response to protein ligands in neurons. Here, we demonstrate for the first time that the NMDA-R is expressed by rat Schwann cells and functions independently and with LRP1 to regulate Schwann cell physiology. The NR1 (encoded by GRIN1) and NR2b (encoded by GRIN2B) NMDA-R subunits were expressed by cultured Schwann cells and upregulated in sciatic nerves following crush injury. The ability of LRP1 ligands to activate ERK1/2 (also known as MAPK3 and MAPK1, respectively) and promote Schwann cell migration required the NMDA-R. NR1 gene silencing compromised Schwann cell survival. Injection of the LRP1 ligands tissue-type plasminogen activator (tPA, also known as PLAT) or MMP9-PEX into crush-injured sciatic nerves activated ERK1/2 in Schwann cells in vivo, and the response was blocked by systemic treatment with the NMDA-R inhibitor MK801. tPA was unique among the LRP1 ligands examined because tPA activated cell signaling and promoted Schwann cell migration by interacting with the NMDA-R independently of LRP1, albeit with delayed kinetics. These results define the NMDA-R as a Schwann cell signaling receptor for protein ligands and a major regulator of Schwann cell physiology, which may be particularly important in peripheral nervous system (PNS) injury. Summary: The NMDA receptor and LRP1 function as co-receptors in Schwann cells, activating cell signaling in response to protein ligands and promoting cell survival and migration.
Behavioural management of aggression in dementia: a randomized controlled trial.

OBJECTIVE To evaluate the efficacy of a brief behaviour management training programme for family carers of patients with dementia and aggressive behaviour. DESIGN A randomized controlled trial of a four-session, community-based behaviour management programme. The primary outcome measure was the Rating Scale for Aggressive Behaviour in the Elderly. PARTICIPANTS 62 patients with dementia, and their co-resident carers. RESULTS There were no significant differences in aggression scores between behaviour management and control groups at follow-up. After adjusting for baseline differences in Rating Scale for Aggressive Behaviour in the Elderly scores, there was a trend towards a reduction in aggressive behaviour in the patients in the behaviour management group compared with those in the control group (F = 3.37, P = 0.071). CONCLUSIONS This study adds to the small evidence base for the effectiveness of behavioural management strategies in dementia.
Postpartum Contraceptive use and Rapid Repeat Pregnancy Among Women who use Substances

ABSTRACT Background: Postpartum contraception is especially important for women who use alcohol and other substances, given the risk of possible rapid repeat pregnancy and prenatal substance exposure. However, little is known about postpartum contraceptive use among women with substance use histories. Objective: To characterize postpartum contraceptive initiation, 24-month continuation, and rapid repeat pregnancy among women who used substances during pregnancy. Methods: This is a secondary analysis of 161 pregnant women who enrolled in a randomized clinical trial to treat substance use in pregnancy and completed at least one follow-up assessment. Women were eligible if they were less than 28 weeks gestation and reported alcohol or illicit drug use within the past 30 days. Participants were recruited from two hospital-based OB/GYN clinics between 2006 and 2010, and completed assessments at delivery and 3-, 12-, and 24-months postpartum. Results: Past 30-day use of any substance (not including tobacco) was 52.4%, 58.3%, and 59.8% at 3-, 12-, and 24-month follow-up, respectively. Marijuana was the most commonly reported illicit substance (as high as 48.1%). Rates of any contraceptive use were 71.3%, 66.7% and 65.3% at 3-, 12-, and 24-month follow-up, respectively; DepoProvera and condoms were the most common methods. Rapid repeat pregnancy occurred in 28% of participants by 24-month follow-up. Conclusions/Importance: Postpartum contraceptive use among substance using women was at or near 70%, which is comparable to other samples of postpartum women. Innovative efforts are needed to promote effective contraceptive use among postpartum women in general and among those who use substances in particular.
Immune responses following experimental human hookworm infection

To characterize the immune response following primary human hookworm infection, an adult volunteer was infected with 50 L3 larvae of Necator americanus, reinfected 27 months later and followed for a further 6 months. Clinical signs, blood picture, ex‐vivo peripheral blood cytokine production (IFN‐γ, IL‐5, IL‐13, IL‐10 to mitogen and hookworm antigen), acute phase proteins (APP) (C‐reactive protein, CRP and α1‐antitrypsin, α1‐AT) and antibody levels were determined. Dermatitis, oedema, mild nausea and abdominal discomfort followed the primary infection. Eosinophil counts peaked early during both infections but remained elevated (∼18%) throughout. Transient production of IL‐5, IL‐13 and APP also followed infection but there were negligible levels of IFN‐γ or IL‐10. The onset of nausea, oedema and the initial rise in CRP, α1‐AT, eosinophilia and IL‐5 coincided (days 13–27) with the late larval migration and early establishment of the preadult worms in the intestine. Apart from the eosinophilia these responses declined to baseline levels within 4 months and were less pronounced on re‐infection.
Linking Medicare capital payments to hospital occupancy rates.

Prologue: How to reimburse hospitals for their capital costs has remained a thorn in the side of the Medicare prospective payment system since its enactment in 1983. Congress initially agreed to pay for the portion of “reasonable” capital costs attributable to a hospital's Medicare patients, while setting a deadline of October 1986 for devising a method of incorporating capital payment into the new system of prospectively determined per case payments (diagnosis-related groups, or DRGs). This deadline has been pushed back several times and now stands at October 1,1991. In the meantime, capital payments to hospitals have been subjected to across-the-board reductions (15 percent in fiscal year 1989) as Congress and the adminstration strive to lower the federal budget deficit In this paper, economists Michael Hemesath and Gregory Pope argue that this current method of saving money is “essentially arbitrary” and propose a means of cutting capital payments through occupancy penalties. They write: “A more equita.
Religion and Medicine I: Historical Background and Reasons for Separation

Religion and medicine have a long, intertwined, tumultuous history, going back thousands of years. Only within the past 200–300 years (less than 5 percent of recorded history) have these twin healing traditions been clearly separate. This series on religion and medicine begins with a historical review, proceeding from prehistoric times through ancient Egypt, Greece, and early Christianity through the Middle Ages, the Renaissance, and the Age of Enlightenment, when the split between religion and medicine became final and complete. Among the many reasons for the continued separation is that religion may either be simply irrelevant to health or, worse, that it may have a number of negative health effects. I review here both opinion and research supporting this claim.
Biochemical Characteristics and PrPSc Distribution Pattern in the Brains of Cattle Experimentally Challenged with H-type and L-type Atypical BSE

Besides the classical form of bovine spongiform encephalopathy (BSE) that has been known for almost three decades, two atypical forms designated H-type and L-type BSE have recently been described. While the main diagnostic feature of these forms is the altered biochemical profile of the accumulated PrPSc, it was also observed in the initial analysis that L-type BSE displays a distribution pattern of the pathological prion protein (PrPSc), which clearly differs from that observed in classical BSE (C-type). Most importantly, the obex region in the brainstem is not the region with the highest PrPSc concentrations, but PrPSc is spread more evenly throughout the entire brain. A similar distribution pattern has been revealed for H-type BSE by rapid test analysis. Based on these findings, we performed a more detailed Western blot study of the anatomical PrPSc distribution pattern and the biochemical characteristics (molecular mass, glycoprofile as well as PK sensitivity) in ten different anatomical locations of the brain from cattle experimentally challenged with H- or L-type BSE, as compared to cattle challenged with C-type BSE. Results of this study revealed distinct differences in the PrPSc deposition patterns between all three BSE forms, while the biochemical characteristics remained stable for each BSE type among all analysed brain areas.
Filtering and segmentation of polarimetric SAR images with Binary Partition Trees

A new multi-scale PolSAR data filtering technique, based on a Binary Partition Tree (BPT) representation of the data, is proposed. Different alternatives for the construction and the exploitation of the BPT for filtering and segmentation are presented. Results with simulated and experimental PolSAR data are presented to shown the capabilities of the BPT-filtering strategy to maintain both spatial details and the polarimetric information.
Polarity detection of sarcastic political tweets

Sarcasm is an activity of saying or writing in such a way that the textual meaning of what is said is opposite of what is meant. Generally, sarcastic sentences are used to express negative feelings. Thus in political polarity detection, it can be used to know the dissatisfaction of people against a particular party, candidate or government and hence considering this other aspects can determine the poll results. This paper presents two algorithms, one to identify a sarcastic tweet and other to perform polarity detection on political sarcastic tweets. It also includes the current approach we are using to identify the sarcastic political tweets and future aspects. It also emphasizes on using the social networking sites and mainly Twitter as a source for predicting political results.
Experimental Investigation of Border Trap Generation in InGaAs nMOSFETs With $\hbox{Al}_{2}\hbox{O}_{3}$ Gate Dielectric Under PBTI Stress

The reliability performance of In<i>x</i>Ga<sub>1-</sub><i>x</i>As n-type metal-oxide-semiconductor field-effect transistors with Al<sub>2</sub>O<sub>3</sub> gate dielectric under positive-bias temperature instability stress is investigated systematically. A model of stress-induced border traps was proposed to interpret all charge pumping and <i>I</i>-<i>V</i> experimental results excellently. The stress-induced border traps include recoverable donor traps and permanent acceptor traps with respective energy densities Δ<i>D</i><sub>SOX</sub><sup>Donor</sup>(<i>E</i>) and Δ<i>D</i><sub>SOX</sub><sup>Acceptor</sup>(<i>E</i>) . The shapes of Δ<i>D</i><sub>SOX</sub><sup>Donor</sup>(<i>E</i>) and Δ<i>D</i><sub>SOX</sub><sup>Acceptor</sup>(<i>E</i>) have been extracted from experimental data. Δ<i>D</i><sub>SOX</sub><sup>Acceptor</sup>(<i>E</i>) mainly distributes in the conduction band of InGaAs with a tail extending to the mid-gap, whereas Δ<i>D</i><sub>SOX</sub><sup>Donor</sup>(<i>E</i>) has a large distribution inside the energy gap and extends to the conduction band. The high density of Δ<i>D</i><sub>SOX</sub><sup>Donor</sup>(<i>E</i>) in the energy gap induces large degradation in the off-current, which is particularly serious when the In composition <i>x</i> is raised to 0.65.
Architecture, Settlement, and Formative Developments in the Equatorial Andes: New Discoveries in the Department of Tumbes, Peru

Abstract The cultural transformations associated with the Formative period are pivotal for understanding the prehistory of the Americas. Over the last five decades, investigations in southwestern Ecuador have provided an early and robust set of archaeological data relating to Archaic-to-Formative transformations as exemplified by the Las Vegas, Valdivia, Machalilla, and Chorrera archaeological traditions. However, recent archaeological research in adjacent zones of the equatorial Andes indicates that the transformations in southwestern Ecuador were paralleled by coeval but distinct developments. Recent (2006–2007) excavations in the Department of Tumbes, Peru, have documented previously unknown Formative transformations, including the development of substantial domestic architecture during the Archaic (ca. 4700–4330 B.C.E.) and early Formative (ca. 3500–3100 B.C.E.), the shift from elliptical pole-and-thatch dwellings to rectangular wattle-and-daub structures at ca. 900–500 B.C.E. , and the construction of public architecture and the establishment of a two-tiered settlement system by ca. 1000–800 B.C.E. These recently discovered archaeological patterns from Tumbes and additional data from southern Ecuador provide the basis for revised comparative perspectives in which southwestern Ecuador is a significant—but no longer the only—vantage point for understanding the evolution of Formative societies in the equatorial Andes.
High Resolution Direction of Arrival (DOA) Estimation Based on Improved Orthogonal Matching Pursuit (OMP) Algorithm by Iterative Local Searching

DOA (Direction of Arrival) estimation is a major problem in array signal processing applications. Recently, compressive sensing algorithms, including convex relaxation algorithms and greedy algorithms, have been recognized as a kind of novel DOA estimation algorithm. However, the success of these algorithms is limited by the RIP (Restricted Isometry Property) condition or the mutual coherence of measurement matrix. In the DOA estimation problem, the columns of measurement matrix are steering vectors corresponding to different DOAs. Thus, it violates the mutual coherence condition. The situation gets worse when there are two sources from two adjacent DOAs. In this paper, an algorithm based on OMP (Orthogonal Matching Pursuit), called ILS-OMP (Iterative Local Searching-Orthogonal Matching Pursuit), is proposed to improve DOA resolution by Iterative Local Searching. Firstly, the conventional OMP algorithm is used to obtain initial estimated DOAs. Then, in each iteration, a local searching process for every estimated DOA is utilized to find a new DOA in a given DOA set to further decrease the residual. Additionally, the estimated DOAs are updated by substituting the initial DOA with the new one. The simulation results demonstrate the advantages of the proposed algorithm.
p-torsion elements in local cohomology modules. II

Gennady Lyubeznik conjectured that if R is a regular ring and a is an ideal of R, then the local cohomology modules H i a (R) have only finitely many associated prime ideals, [Ly1, Remark 3.7 (iii)]. While this conjecture remains open in this generality, several results are now available: if the regular ring R contains a field of prime characteristic p > 0, Huneke and Sharp showed in [HS] that the set of associated prime ideals of H i a (R) is finite. If R is a regular local ring containing a field of characteristic zero, Lyubeznik showed that H i a (R) has only finitely many associated prime ideals, see [Ly1] and also [Ly2, Ly3]. Recently Lyubeznik has also proved this result for unramified regular local rings of mixed characteristic, [Ly4]. In [Hu] Craig Huneke first raised the following question: for a Noetherian ring R, an ideal a ⊂ R, and a finitely generated R-module M , is the number of associated primes ideals of H i a (M) always finite? For some of the work on this problem, we refer the reader to the papers [BL, BRS, He] in addition to those mentioned above. In [Si] we constructed an example of a hypersurface R for which a local cohomology module H3 a (R) has p-torsion elements for every prime integer p, and consequently has infinitely many associated prime ideals. Since this is the only known source of infinitely many associated prime ideals so far, it is worthwhile to investigate whether similar techniques may yield an example of a regular ring R for which a local cohomology module H i a (R) has p-torsion elements for every prime integer p. This leads to some very intriguing questions as we shall see in this paper. Our results thus far support Lyubeznik’s conjecture that local cohomology modules of all regular rings have only finitely many associated prime ideals. Let R be a polynomial ring over the integers and Fi, Gi be elements of R for which