Miracle-dz/UniFAR-FTUs huggingface dataset:
Strategies for Resynchronization of Ovulation and Timed AI

Many confinement-based dairy systems in the U.S. have adopted systematic synchronization protocols and timed artificial insemination (TAI) for submitting cows for first postpartum AI service (Caraviello et al., 2006). Although reliance on synchronization of ovulation and TAI for improving service rate to first AI service reduces the impact of poor estrous detection, the improved AI submission rate to first TAI often is followed by a time lag exceeding 60 d before cows failing to conceive are detected and reinseminated. Because conception rates to TAI for dairy cows managed in confinement-based systems in the U.S. are reported to be 40% or less (Pursley et al., 1997a,b; Fricke et al., 1998; Jobst et al., 2000), 60% or more of the cows will fail to conceive and therefore require a resynchronization strategy for aggressively initiating subsequent AI services. Methods for early detection of nonpregnancy coupled with hormonal resynchronization systems that program nonpregnant cows to receive subsequent TAI services are now being developed and assessed so that systematic reproductive management programs can be implemented to aggressively manage reproduction (Fricke, 2002). A wide array of reproductive management strategies have been developed to fit the various dairy production systems that are found around the world, and the diversity among these strategies has been reviewed elsewhere (Lucy et al., 2004). Although studies have been conducted to resynchronize behavioral estrus among groups of previously inseminated cows (Chenault et al., 2003), the objective of this review is to overview strategies for resynchronization of ovulation that allow for TAI of cows failing to conceive to a prior AI service.
An Overview of Efficiency and Loss Characterization of Fractional Horsepower Motors

This paper presents techniques for testing fractional horsepower (FHP) induction and brushless dc motors. The procedures for segregation of losses in these motors are presented. The issues encountered in testing FHP motors are discussed, and guidelines are provided to avert the issues. This paper also provides insights into understanding the test procedures outlined in the IEEE 114 Standard.
The Lost Squares of Dr. Franklin: Ben Franklin's Missing Squares and the Secret of the Magic Circle

Three of Franklin's mathematical diagrams are widely reprinted. Adorning the cover of Oystein Ore's splendid Invitation to Number Theory is the 'magic circle'. Franklin's squares still appear today in popular mathematics books such as Theoni Pappas's Joy of Mathematics and Jan Gullberg's encyclopedic Mathematics: From the Birth of Numbers. When the latter tome was reviewed in the MONTHLY [2], out of thousands of diagrams and drawings, only two figures were reproduced there, and one of these was a Franklin square. What is so special about it? Writing in Historia Mathematica some years ago, Edward Hogan stated:
Survival of Trypanosoma brucei in the Tsetse Fly Is Enhanced by the Expression of Specific Forms of Procyclin

African trypanosomes are not passively transmitted, but they undergo several rounds of differentiation and proliferation within their intermediate host, the tsetse fly. At each stage, the survival and successful replication of the parasites improve their chances of continuing the life cycle, but little is known about specific molecules that contribute to these processes. Procyclins are the major surface glycoproteins of the insect forms of Trypanosoma brucei. Six genes encode proteins with extensive glutamic acid–proline dipeptide repeats (EP in the single-letter amino acid code), and two genes encode proteins with an internal pentapeptide repeat (GPEET). To study the function of procyclins, we have generated mutants that have no EP genes and only one copy of GPEET. This last gene could not be replaced by EP procyclins, and could only be deleted once a second GPEET copy was introduced into another locus. The EP knockouts are morphologically indistinguishable from the parental strain, but their ability to establish a heavy infection in the insect midgut is severely compromised; this phenotype can be reversed by the reintroduction of a single, highly expressed EP gene. These results suggest that the two types of procyclin have different roles, and that the EP form, while not required in culture, is important for survival in the fly.
Epstein–Barr virus nuclear protein EBNA3C is required for cell cycle progression and growth maintenance of lymphoblastoid cells

Epstein–Barr virus (EBV) infection converts primary human B cells into continuously proliferating lymphoblastoid cell lines (LCLs). To examine the role of EBV nuclear antigen (EBNA) 3C in the proliferation of LCLs, we established LCLs infected with an EBV recombinant that expresses EBNA3C with a C-terminal fusion to a 4-hydroxytamoxifen (4HT)-dependent mutant estrogen receptor, E3C–HT. In the presence of 4HT, LCLs expressed the E3C–HT protein and grew like WT LCLs. When E3C–HT EBV-infected LCLs were transferred to medium without 4HT, E3C–HT protein slowly disappeared, and the LCLs gradually ceased growing. WT EBNA3C expression from an oriP plasmid transfected into E3C–HT LCLs protected the LCLs from growth arrest in medium without 4HT, whereas expression of EBNA3A or EBNA3B did not. The expression of other EBNA proteins and of LMP1, CD21, CD23, and c-myc was unaffected by EBNA3C inactivation. However, EBNA3C inactivation resulted in the accumulation of p16INK4A, a decrease in the hyperphosphorylated form of the retinoblastoma protein, and a decrease in the proportion of cells in S or G2/M phase. These results indicate that EBNA3C has an essential role in cell cycle progression and the growth maintenance of LCLs.
How might epigenetic dysregulation in early embryonic life contribute to autism spectrum disorder?

The potential for non-genetic susceptibility to mediate part of the risk of autism spectrum disorder (ASD) has prompted a number of studies to date, all showing evidence for epigenetic differences characterizing the individuals with ASD. The modest differences in DNA methylation observed have indicated an underlying cellular mosaicism for epigenetic dysregulation. The studies to date have not comprehensively addressed potential confounding issues like cell subcomposition differences, transcriptional and DNA sequence variability. Additionally, it is possible that mutations in protein-coding genes encoding transcriptional and chromatin regulatory proteins lead to the epigenetic changes in a subset of individuals with ASD. More definitive studies are now needed to allow higher confidence insights into epigenetic events occurring in early embryogenesis in individuals with ASD.
Climate Change Relocation as an Adaptation Strategy: from Taboo to Opportunity

Relocation is often taboo among policy makers and planners due to its political, social, and ethical connotations, and although increasingly mentioned as one of the potential climate change adaptation strategies, it mostly adheres to rhetoric with limited discussion of its actual implementation. Scientific study and observation indicate the imminence of climate change impacts, many of which may exceed the adaptive capacity of vulnerability hotspots. Therefore, it is imperative to reassess this response option in the light of its past negative reputation, the success of current initiatives, and decision makers’ evolving perception of relocation as an adaptation option. The main objective of this dissertation research is to determine the need for, interest in, and prospects for community relocations as an adaptation option; explore ways to address limitations associated with this alternative, and identify opportunities that could emerge from the relocation process. This study reviews experiences from the past and current relocation efforts and gauges the current level of interest in and support for this adaptation option among policy makers and planners. It also provides conceptual models the relocation scenario, its digitalized simulation, the Climate Change Relocation Leaf, and the Relocation Suitability Index designed to help communities, policy makers and planners explore this alternative. The research commences with a comprehensive literature review of theoretical knowledge, past experiences, current case studies, and the existing state of institutional, political, and social perspectives related to climate change migration and relocation. It continues with a comparative content analysis of climate change adaptation plans to elucidate the relocation rhetoric utilized in the selected texts at what frequency and in what context. Next, the study represents the climate change relocation models and a scenario developed to engage decision-makers and stakeholders in assessing the need for and possibility of relocation. Lastly, the project concludes with the development of a conceptual and tabular framework for the Relocation Suitability Index and subsequent simulation designed to compare possible relocation host sites systematically based on their absorption capacity.
Th17 cells in immunity and autoimmunity

The primary function of Th17 cells appears to be the clearance of extracellular pathogens during infections. However, Th17 cells also promote inflammation and have been implicated in the pathogenesis of many experimental autoimmune diseases and human inflammatory conditions. Transforming growth factor β (TGFβ) is a critical differentiation factor for the generation of regulatory T (T-reg) cells, whereas the combination of interleukin 6 (IL6) and TGFβ induces the differentiation of pathogenic Th17 cells. Therefore, it is proposed that at the steady state (in the absence of any inflammatory stimuli), TGFβ, which is produced by various cells types including naturally occurring T-reg (nT-reg) cells, encourages the generation of induced T-reg (iT-reg) cells, which together with nT-reg cells keep autoreactive T cells under check. IL6, an acute phase protein produced by the activated immune system, inhibits the function of T-reg cells and instead promotes the differentiation of Th17 cells. Thus, IL6 plays a pivotal role in dictating the balance between the generation of T-reg and Th17 cells. This reciprocal relationship between T-reg and Th17 cells is further supported by the results obtained in IL6−/− mice, which show a severe defect in the generation of Th17 cells and increased numbers of T-reg cells in the peripheral repertoire.
An Interview-Based User Study on the use of Visualizations for Folder Browsing

Hierarchically structured data collections often need to be visualized for the purposes of digital information management and presentation. File browsing, in particular, has an inherent hierarchical structure and plays an important role in the context of personal information management (PIM). A multitude of file browsers are nowadays available, offering different functionalities, while users adopt diverse practices and habits for browsing activities. In this paper, we investigate these aspects to obtain insights into their advantages and disadvantages and suggest solutions in the area of PIM, as well as in other domains employing similar visualization paradigms. The presented study focuses on the two most widespread visualizations used by file browsers, the indented list and zoomable interface paradigms, and assesses their effectiveness for various tasks and contexts, both by exploiting results on existing evaluations on hierarchy visualizations and folder hierarchy visualizations in particular, and by conducting an interview-based user study.
Neogene and Quaternary fossil remains of beaked whales (Cetacea, Odontoceti, Ziphiidae) from deep-sea deposits off Crozet and Kerguelen islands, Southern Ocean

ABSTRACT Although a high number of extant beaked whale species (Cetacea, Odontoceti, Ziphiidae) live in the Southern Ocean and neighbouring areas, only little is known about the past occupation of the region by these highly specialized, deep diving and echolocating cetaceans. Recently, longline fishing activities along the seafloor at depths of 500–2000 m off the sub-antarctic Crozet and Kerguelen islands, Indian sector of Southern Ocean, resulted in the accessory “capture” of tens of ziphiid fossil cranial remains. Our description and comparison of the best-preserved and most diagnostic crania from this sample lead to the identification of more than eight species in at least seven genera: the hyperoodontines Africanacetus ceratopsis, Khoikhoicetus kergueleni n. sp. , Hyperoodontinae indet. aff. Africanacetus, and Mesoplodon sp. aff. Mesoplodon layardii, the ziphiines Izikoziphius rossi and Ziphius sp. , and the ziphiids indet. Nenga sp. aff. Nenga meganasalis and Xhosacetus hendeysi. Unsurprisingly, with at least four species in common (A. ceratopsis, Izikoziphius rossi, X. hendeysi, and Ziphius sp.), the assemblage displays high similarities with assemblages described from deep-sea deposits off South Africa, providing thus new data on the palaeogeographic distribution of several extinct species and indicating a roughly similar geochronological age for at least a part of the assemblages. The limited amount of data available points to a pre-Pliocene age for a large part of the Crozet-Kerguelen assemblage, suggesting a relatively early, Miocene colonization of the Southern Ocean by crown ziphiids. Contrastingly, 14C radiometric dating of two specimens of Mesoplodon sp. aff. Mesoplodon layardii yielded latest Pleistocene-earliest Holocene ages. These results reveal the presence either of an extinct species of Mesoplodon in the Southern Ocean only a few thousands years ago, or of an up-to-now unidentified extant species closely related to the strap-toothed whale M. layardii.
The Correlation between Serum Level of Leptin and Troponin in Children with Major Beta-Thalassemia

Background Polypeptide hormone Leptin suppresses inflammation in the heart muscle and protects heart from diseases. The purpose of this study is to evaluate the relationship between leptin and troponin serum levels with cardiac involvement in patients with major beta thalassemia. Materials and Methods In this cross-sectional study, 70 children with major thalassemia were selected. Two ml blood was taken as sample from all children and after separating serum; the samples were maintained in -20°C temperature. Then, regarding cold chain conditions, the sample were sent to the Biochemistry Lab. Afterwards, leptin and troponin serum levels with the relevant kits and BMI were measured in all children, and information about age and gender was recorded. Collected data were analyzed with SPSS. Results The mean of leptin in girls and boys were 2.47 ± 3.13 and 0.96 ± 1.08 respectively which showed a significant difference (t=2.74, p =0.009). A significant correlation was also observed between BMI and leptin (r = 0.374, P = 0.002). Another significant association was found between leptin and age (r = 0.248, P = 0.041). However, a significant inverse correlation between serum ferritin and age (r = - 0.607, P = 0.0001) was discovered. No correlation was found between leptin, troponin, and ferritin. Conclusion Since Leptin increases with the advent of cardiac involvement and independent from troponin T, it can be a predictive marker of cardiac involvement in patients with major beta thalassemia.
Breast cancer: assessing response to neoadjuvant chemotherapy by using US-guided near-infrared tomography.

PURPOSE To assess initial breast tumor hemoglobin (Hb) content before the initiation of neoadjuvant chemotherapy, monitor the Hb changes at the end of each treatment cycle, and correlate these findings with tumor pathologic response. MATERIALS AND METHODS The HIPAA-compliant study protocol was approved by the institutional review boards of both institutions. Written informed consent was obtained from all patients. Patients who were eligible for neoadjuvant chemotherapy were recruited between December 2007 and May 2011, and their tumor Hb content was assessed by using a near-infrared imager coupled with an ultrasonography (US) system. Thirty-two women (mean age, 48 years; range, 32-82 years) were imaged before treatment, at the end of every treatment cycle, and before definitive surgery. The patients were graded in terms of their final pathologic response on the basis of the Miller-Payne system as nonresponders and partial responders (grades 1-3) and near-complete and complete responders (grades 4 and 5). Tumor vascularity was assessed from total Hb (tHb), oxygenated Hb (oxyHb), and deoxygenated Hb (deoxyHb) concentrations. Tumor vascularity changes during treatment were assessed from percentage tHb normalized to the pretreatment level. A two-sample two-sided t test was used to calculate the P value and to evaluate statistical significance between groups. Bonferroni-Holm correction was applied to obtain the corrected P value for multiple comparisons. RESULTS There were 20 Miller-Payne grade 1-3 tumors and 14 grade 4 or 5 tumors. Mean maximum pretreatment tHb, oxyHb, and deoxyHb levels were significantly higher in grade 4 and 5 tumors than in grade 1-3 tumors (P = .005, P = .008, and P = .017, respectively). The mean percentage tHb changes were significantly higher in grade 4 or 5 tumors than in grade 1-3 tumors at the end of treatment cycles 1-3 (P = .009 and corrected P = .009, P = .002 and corrected P = .004, and P < .001 and corrected P < .001, respectively). DISCUSSION These findings indicate that initial tumor Hb content is a strong predictor of final pathologic response. Additionally, the tHb changes during early treatment cycles can further predict final pathologic response.
A general model for the evolution of recombination.

A general representation of multilocus selection is extended to allow recombination to depend on genotype. The equations simplify if modifier alleles have small effects on recombination. The evolution of such modifiers only depends on how they alter recombination between the selected loci, and does not involve dominance in modifier effects. The net selection on modifiers can be found explicitly if epistasis is weak relative to recombination. This analysis shows that recombination can be favoured in two ways: because it impedes the response to epistasis which fluctuates in sign, or because it facilitates the response to directional selection. The first mechanism is implausible, because epistasis must change sign over periods of a few generations: faster or slower fluctuations favour reduced recombination. The second mechanism requires weak negative epistasis between favourable alleles, which may either be increasing, or held in check by mutation. The selection (si) on recombination modifiers depends on the reduction in additive variance of log(fitness) due to linkage disequilibria (v1 < O), and on non-additive variance in log(fitness) (V'2, V'3. for epistasis between 2, 3. loci). For unlinked loci and pairwise epistasis, si = --(v1 +4V2/3)deltar, where deltar is the average increase in recombination caused by the modifier. The approximations are checked against exact calculations for three loci, and against Charlesworth's analyses of mutation/selection balance (1990), and directional selection (1993). The analysis demonstrates a general relation between selection on recombination and observable components of fitness variation, which is open to experimental test.
Constraints on the Physics of Type Ia Supernovae from the X-Ray Spectrum of the Tycho Supernova Remnant

In this paper we use high-quality X-ray observations from XMM-Newton and Chandra to gain new insights into the explosion that originated Tycho's supernova 433 yr ago. We perform a detailed comparison between the ejecta emission from the spatially integrated X-ray spectrum of the supernova remnant and current models for Type Ia supernova explosions. We use a grid of synthetic X-ray spectra based on hydrodynamic models of the evolution of the supernova remnant and nonequilibrium ionization calculations for the state of the shocked plasma. We find that the fundamental properties of the X-ray emission in Tycho are well reproduced by a one-dimensional delayed detonation model with a kinetic energy of ~1.2 × 1051 ergs. All the other paradigms for Type Ia explosions that we have tested, including one-dimensional deflagrations, pulsating delayed detonations, and sub-Chandrasekhar explosions, as well as deflagration models calculated in three dimensions, fail to provide a good approximation of the observed ejecta emission. Our results require that the supernova ejecta retain some degree of chemical stratification, with Fe peak elements interior to intermediate-mass elements. This strongly suggests that a supersonic burning front (i.e., a detonation) must be involved at some stage in the physics of Type Ia supernova explosions.
Oxidative mechanisms utilized by human neutrophils to destroy Escherichia coli.

Serum-opsonized bacteria are efficiently ingested and killed by neutrophils within the phagocytic vacuole, where they are exposed to an array of reactive oxygen metabolites and toxic lysosomal components. Although bacteria may be destroyed by oxygen-independent mechanisms alone, many types of bacteria are not killed effectively unless they are attacked by oxygen metabolites. However, the apparent inability of extracellular scavengers, or inhibitors, of oxygen metabolites to gain access to the phagocytic vacuole makes this system difficult to evaluate. Therefore, we investigated the ability of neutrophils triggered with phorbol myristate acetate to destroy unopsonized E. coli in a serum-free model system. Neutrophils incubated with phorbol myristate acetate at a cell-to-bacteria ratio of 1:4 caused a greater than 95% reduction in colony-forming units (CFU) of E. coli in 60 min at 37 degrees C. Destruction of E. coli by the stimulated neutrophils was dependent on neutrophil number, stimuli concentration, and the incubation period. The neutrophil-mediated bactericidal effect was stimulated by superoxide dismutase, but was inhibited by catalase, azide, or compounds known to scavenge hypochlorous acid. Although stimulated neutrophils can generate long-lived endogenous N- chloroamines , these compounds did not play a direct role in destruction of E. coli in our model system. However, in the presence of exogenous iodide, endogenous N- chloroamines exerted a powerful bactericidal effect. Finally, neutrophils triggered with opsonized zymosan could also mediate E. coli destruction by a qualitatively similar process. Thus, we have demonstrated that neutrophils have the potential to utilize the myeloperoxidase system to generate bactericidal quantities of a species with characteristics similar to, if not identical with, hypochlorous acid.
Medical therapy to reduce postoperative Crohn's disease recurrence

Clinical recurrence of Crohn's disease after surgical resection is a significant problem, with reported rates as high as 55% at 5 yr and 76% at 15 yr. Specific factors that predispose to postoperative recurrence of Crohn's disease have not been well defined. In addition, the underlying pathophysiology of recurrent disease and the reason for its localization to the neoterminal ileum are not well understood. Various operative techniques have been evaluated but none, aside from formation of an ostomy, has been shown to reduce the risk of recurrence. In contrast, there is increasing evidence that postoperative medical therapy has the potential to decrease the risk of postoperative recurrence.Historically, sulfasalazine may have a modest effect on reducing postoperative recurrence of ileal or ileocolonic disease. However, 5-ASA preparations that can selectively deliver mesalamine to the small bowel or anastomotic margin should be more effective. Indeed, in several studies and as confirmed by a meta-analysis, mesalamine has been demonstrated to reduce significantly postoperative recurrence of Crohn's disease. Metronidazole and 6-mercaptopurine or azathioprine also seem to be of benefit in postoperative prophylaxis of disease recurrence, but additional controlled studies are required to define better the efficacy and dose-response of these agents. Corticosteroids are ineffective at reducing postoperative recurrence.