bluuebunny/crossref_metadata_2025_split huggingface dataset:
antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline
Authors: Blin Kai , Shaw Simon , Steinke Kat , Villebro Rasmus , Ziemert Nadine , Lee Sang Yup , Medema Marnix H , Weber Tilmann 
Published: April 2019

Abstract
Secondary metabolites produced by bacteria and fungi are an important source of antimicrobials and other bioactive compounds. In recent years, genome mining has seen broad applications in identifying and characterizing new compounds as well as in metabolic engineering. Since 2011, the ‘antibiotics and secondary metabolite analysis shell—antiSMASH’ (https://antismash.secondarymetabolites.org) has assisted researchers in this, both as a web server and a standalone tool. It has established itself as the most widely used tool for identifying and analysing biosynthetic gene clusters (BGCs) in bacterial and fungal genome sequences. Here, we present an entirely redesigned and extended version 5 of antiSMASH. antiSMASH 5 adds detection rules for clusters encoding the biosynthesis of acyl-amino acids, β-lactones, fungal RiPPs, RaS-RiPPs, polybrominated diphenyl ethers, C-nucleosides, PPY-like ketones and lipolanthines. For type II polyketide synthase-encoding gene clusters, antiSMASH 5 now offers more detailed predictions. The HTML output visualization has been redesigned to improve the navigation and visual representation of annotations. We have again improved the runtime of analysis steps, making it possible to deliver comprehensive annotations for bacterial genomes within a few minutes. A new output file in the standard JavaScript object notation (JSON) format is aimed at downstream tools that process antiSMASH results programmatically.
Radiosurgical Management of Patients With Persistent or Recurrent Cushing Disease After Prior Transsphenoidal Surgery: A Management Algorithm Based on a 25-Year Experience
Authors: Hughes Joshua D , Young William F , Chang Alice Y , Link Michael J , Garces Yolanda I , Laack Nadia N , Thompson Geoffrey B , Pollock Bruce E 
Published: April 2019

Abstract

BACKGROUND
Patients with persistent or recurrent Cushing disease (CD) after prior transsphenoidal surgery require further treatment to reduce the disease's metabolic consequences.

OBJECTIVE
To assess patient outcomes after stereotactic radiosurgery (SRS) for persistent or recurrent CD from adrenocorticotropin hormone (ACTH)-secreting pituitary adenomas and propose a management algorithm.

METHODS
Retrospective review of 38 patients without prior radiation treatment having SRS for ACTH-secreting pituitary adenomas from 1990 to 2015. Favorable outcome was defined as biochemical remission and tumor growth control. Patients were evaluated separately if they underwent bilateral adrenalectomy (Adx).

RESULTS
Twenty patients (53%) were treated with Adx and SRS (median margin dose, 25 Gy) and 18 patients (47%) received SRS alone (median margin dose, 22.5 Gy). Median follow-up after SRS was 76 mo. Of patients undergoing Adx, 18/20 (90%) had a favorable outcome. Two patients (10%) had tumor growth requiring additional treatment. A favorable outcome was achieved in 13/18 patients (72%) having SRS alone (median, 14 mo; interquartile range, 8-23). Five patients (28%) required additional treatment due to persistent hypercortisolemia (n = 4) or hypercortisolemia and tumor growth (n = 1). Favorable outcomes were more frequent in the Adx and SRS group at 1 yr (100% vs 33%; P < .001) and 3 yr (100% vs 62%; P < .01), but no different at 5 yr (88% vs 77%; P = .63).

CONCLUSION
SRS was effective for patients with persistent or recurrent CD. Patients with mild to moderate CD can be safely managed with SRS alone; patients with severe CD should be considered for Adx with either concurrent SRS or SRS performed at a later date if tumor growth occurs.
Image-Guided, Linac-Based, Surgical Cavity-Hypofractionated Stereotactic Radiotherapy in 5 Daily Fractions for Brain Metastases
Authors: Soliman Hany , Myrehaug Sten , Tseng Chia-Lin , Ruschin Mark , Hashmi Ahmed , Mainprize Todd , Spears Julian , Das Sunit , Yang Victor , da Costa Leodante , Maralani Pejman , Heyn Chris , Atenafu Eshetu G , Sahgal Arjun 
Published: April 2019

Abstract

BACKGROUND
Cavity stereotactic radiotherapy has emerged as a standard option following resection of brain metastases. However, the optimal approach with either single-fraction or hypofractionated stereotactic radiotherapy (HSRT) remains a significant question.

OBJECTIVE
To report outcomes for 5-fraction HSRT to the surgical cavity, based on contouring according to a recently reported international consensus guideline.

METHODS
Patients treated with cavity HSRT were identified from a prospective institutional database. Local brain control (LC), distant brain failure (DBF), leptomeningeal disease (LMD), and overall survival rates were determined. Univariate and multivariable analyses were performed on potential predictive factors.

RESULTS
One hundred thirty-seven cavities in 122 patients were treated at a median total dose of 30 Gy (range, 25-35 Gy). The median follow-up was 16 mo (range, 1-60 mo). Nonsmall cell lung cancer was the most common histology (44%), followed by breast cancer (21%). In 57% of surgical cavities, the preoperative tumor diameter was >3 cm. One-year LC, DBF, LMD, and overall survival rates were 84%, 45%, 22%, and 62%, respectively. Multivariable analyses identified colorectal (hazard ratio [HR] 4.1, P = .0066) and melanoma (HR 2.4, P = .012) metastases as predictors of local recurrence; preoperative tumor diameter >2 cm (HR 8.9, P = .012) and absence of targeted therapy (HR 4.4, P = .03) as predictors of DBF; and breast cancer histology (HR 2.1, P = .05) and subtotal resection (HR 2.6, P = .009) as predictors of LMD. Symptomatic radiation necrosis was observed in 7 patients (6%).

CONCLUSION
High rates of LC were observed following this 5-fraction HSRT regimen. Superiority as compared to single-fraction SRS requires a randomized trial.
Risk of First Hemorrhage of Brain Arteriovenous Malformations During Pregnancy: A Systematic Review of the Literature
Authors: Davidoff Christopher L , Lo Presti Anna , Rogers Jeffrey M , Simons Mary , Assaad Nazih N A , Stoodley Marcus Andrew , Morgan Michael Kerin 
Published: April 2019

Abstract

BACKGROUND
Recommendations on the management of brain arteriovenous malformations (bAVM) with respect to pregnancy are based upon conflicting literature.

OBJECTIVE
To systematically review the reported risk and annualized rate of first intracranial hemorrhage (ICH) from bAVM during pregnancy and puerperium.

METHODS
MEDLINE, EMBASE, and Scopus databases were searched for relevant articles in English published before April 2018. Studies providing a quantitative risk of ICH in bAVM during pregnancy were eligible.

RESULTS
From 7 initially eligible studies, 3 studies met the criteria for providing quantitative risk of first ICH bAVM during pregnancy. Data from 47 bAVM ICH during pregnancy across 4 cohorts were extracted for analysis. Due to differences in methodology and definitions of exposure period, it was not appropriate to combine the cases. The annualized risk of first ICH during pregnancy for these 4 cohorts was 3.0% (95% confidence interval [CI]: 1.7-5.2%); 3.5% (95% CI: 2.4-4.5%); 8.6% (95% CI: 1.8-25%); and 30% (95% CI: 18-49%). Only the last result from the last cohort could be considered significantly increased in comparison with the nonpregnant period (relative rate 6.8, 95% CI: 3.6-13). The limited number of eligible studies and variability in results highlighted the need for enhanced rigor of future research.

CONCLUSION
There is no conclusive evidence of an increased risk of first hemorrhage during pregnancy from bAVM. Because advice to women with bAVM may influence the management of pregnancy or bAVM with significant consequences, we believe that a retrospective multicenter, case crossover study is urgently required.
Brain Structure, Connectivity, and Cognitive Changes Following Revascularization Surgery in Adult Moyamoya Disease
Authors: Kazumata Ken , Tha Khin Khin , Tokairin Kikutaro , Ito Masaki , Uchino Haruto , Kawabori Masahito , Sugiyama Taku 
Published: April 2019

Abstract

BACKGROUND
The effect of the combined direct/indirect revascularization surgery in Moyamoya disease has not been evaluated sufficiently with regard to cognitive function, brain microstructure, and connectivity.

OBJECTIVE
To investigate structural and functional changes following revascularization surgery in patients with moyamoya disease (MMD) through a combined analysis of brain morphology, microstructure, connectivity, and neurobehavioral data.

METHODS
Neurobehavioral and neuroimaging examinations were performed in 25 adults with MMD prior to and >12 mo after revascularization surgery. Cognitive function was investigated using the Wechsler Adult Intelligence Scale-III, Trail-Making Test, Wisconsin Card Sorting Test, Continuous Performance Test, Stroop test, and Wechsler Memory Scale. We assessed white matter integrity using diffusion tensor imaging, brain morphometry using magnetization-prepared rapid gradient-echo sequences, and brain connectivity using resting-state functional magnetic resonance imaging (MRI).

RESULTS
Cognitive examinations revealed significant changes in the full-scale intelligence quotient (IQ), performance IQ (PIQ), perceptual organization (PO), processing speed, and Stroop test scores after surgery (P < .05). Enlargement of the lateral ventricle, volume reductions in the corpus callosum and subcortical nuclei, and cortical thinning in the prefrontal cortex were also observed (P < .05). Fractional anisotropy in the white matter tracts, including the superior longitudinal fasciculus, increased 2 to 4 yr after surgery, relative to that observed in the presurgical state (P < .05). Resting-state brain connectivity was increased predominantly in the fronto-cerebellar circuit and was positively correlated with improvements in PIQ and PO (P < .05).

CONCLUSION
Revascularization surgery may improve processing speed and attention in adult patients with MMD. Further, multimodal MRI may be useful for detecting subtle postsurgical brain structural changes, reorganization of white matter tracts, and brain connectivity alterations.
Optimal taxation with unobservable investment in human capital
Authors: Reis Catarina 
Published: April 2019

Abstract
In a Ramsey model of optimal taxation, if human capital investment can be observed separately from consumption, it is optimal not to distort human or physical capital accumulation in the long run, and only labour income taxes should be used. However, in reality the government can’t always distinguish between investment in human capital and pure consumption, so a tax on labour or consumption will necessarily tax human capital. We find that when investment in human capital is unobservable, the optimal policy is to tax human capital at a positive rate, even in the long run. Whether physical capital should be taxed or not depends on its degree of complementarity with human capital versus labour.
Learning to Fly
Authors: Vang Chia Youyee 
Published: April 2019

Abstract
Once selected for pilot training, most participants entered the CIA’s covert Project Water Pump with much excitement, but chapter 3 reveals that they subsequently went through a tumultuous process. Surviving pilots identified internal and external factors that influenced how well they progressed through the aviation program. Academic background helped some to perform well in ground school, especially in learning English. Their narratives, however, suggest that academic abilities alone did not determine who would succeed in learning to fly. Physical and mental health conditions often impacted their training experiences. Surviving pilots describe the obstacles they confronted when interacting with instructors and recall that trainees and instructors generally did not socialize together because of language barriers, as well as a culture of Americans and Lao regarding Hmong as inferior. Instructor pilot narratives unveiled an unorthodox training program that required flexibility from all involved.
Widowhood
Authors: Vang Chia Youyee 
Published: April 2019

Abstract
Chapter 5 reveals that pilots’ salaries greatly improved their families’ livelihoods. Following the death of a pilot, however, his widow and children confronted significant challenges. Widows revealed when they were young women, corrupt military officers and in-laws often denied them full death benefits. The women shared heartfelt memories of their husbands and talked about the moment when they learned about their husbands’ deaths. Some of the pilots were killed in action, whereas others died in aviation accidents of various causes. Regardless of the circumstances by which they had become widows, the wives were filled with conflicting sentiments about the losses and suffering caused by the Secret War. For many, the wounds remain and time has not eased their pain.
Escape
Authors: Vang Chia Youyee 
Published: April 2019

Abstract
Chapter 7 explores the chaotic air evacuation from Long Cheng to Udorn air base in Thailand in early May 1975, in which throngs of Hmong fought to get on planes intended for Hmong military leadership and some selected others. It describes the subsequent flight of thousands more Hmong who were not fortunate enough to gain exit in the airlift; those left behind feared retribution from the communist Pathet Lao regime for having aligned with the United States. The chapter discusses refugee life in Thai camps such as Ban Vinai and the difficult decisions that escapees had to make about resettling elsewhere, since they could not remain in the camps permanently. Some refugees describe the process of finding sponsors for their resettlement in the United States, and a prisoner of war tells how decreased surveillance enabled him to slip away and cross the Mekong River to freedom.
Debunking and Vindicating in Moral Psychology
Authors: Nichols Shaun 
Published: April 2019

Abstract
One way that cognitive science can inform our metaphysical views is by explaining why we have the metaphysical views that we do. Psychological explanations can serve to debunk our intuitive metaphysical commitments when the commitments derive from an epistemically defective process. But psychological explanations can also serve to vindicate our intuitive commitments when they derive from epistemically proper processes. This chapter explores both debunking and vindicating arguments for the belief in moral objectivity. The debunking argument draws on work suggesting that the belief in objectivity is generated from epistemically defective emotional/motivational processes. The vindicatory argument draws on the finding that beliefs about consensus correlate with beliefs about objectivity, and argues that a rational learner would often be right to take consensus information as evidence regarding objectivity.
Santuario de Chimayó
Authors: Graziano Frank 
Published: April 2019

Abstract
After a summary of the santuario’s history, the Christ of Esquipulas is discussed in relation to the Guatemalan image by the same name and to other Black Christs in the region. The use of holy dirt at the santuario is then considered together with miracles attributed to it. The subsequent section discusses aesthetic and spiritual emotional reactions to the interior of the santuario chapel. Also described and analyzed are Holy Week events at the santuario, including the Penitentes’ participation; pilgrimage and the annual Pilgrimages for Vocations; and the murder in 2000 of two teenage pilgrims to the santuario. The chapter concludes with a visiting guide, including directions to historic churches in the area.
Churches along the Southern Río Grande
Authors: Graziano Frank 
Published: April 2019

Abstract
After a brief survey of the historic churches in Tomé, Socorro, and surrounding areas, the chapter focuses on Our Lady of Purification (Nuestra Señora de la Candelaria) in Doña Ana. The emphasis is on the restoration of the church in the 1990s, and on the training program for at-risk youth that provided restoration workers. Attitudes toward adobe restoration among local parishioners are also treated. As this tour continues southward it encompasses, among other churches, San José in La Mesa, where depopulation combined with Mexican immigration has changed the nature of the congregation. The Mission Trail in El Paso is also briefly mentioned. Visiting information is integrated throughout the chapter.
St. Joseph Apache Mission, Mescalero
Authors: Graziano Frank 
Published: April 2019

Abstract
The chapter opens with discussion of native Catholicism among the Apache, and of the syncretic church imagery epitomized by the Apache Christ behind the altar. The discussion then pursues the “rebuild my church” mandate that St. Francis received in a vision and the application of the same by Franciscans and others who undertook the restoration of the huge stone church and the congregation in Mescalero. The discussion of a trainee program at this and other sites introduces a section regarding the influence of church restoration on the alcoholism and sobriety of one of the workers. The chapter then discusses the difficulties of transition from Franciscan to diocesan pastorship. It concludes with a historical section on the freed Chiricahua prisoners of war who settled at Mescalero, and on Father Albert Braun, whose vision and initiative resulted in the construction of St. Joseph. The chapter includes a visiting guide.
One Nation, Two Realities
Authors: Marietta Morgan , Barker David C. 
Published: April 2019

Abstract
Is climate change real? Does racism still determine who gets ahead? Is sexuality innate? Do immigration and free trade help or hurt the economy? Does gun control reduce violence? Are false convictions common? On these and many other basic questions of fact, Americans are deeply divided. How did this happen? What does it mean? And is there anything we can do about it? Drawing upon several years of original survey data and experiments, Marietta and Barker reach a number of enlightening and provocative conclusions. Among them is that dueling fact perceptions are not so much a result of hyper-partisanship or media propaganda as they are of simple value differences and deepening distrust of authorities. The educated—on both the Left and Right—carry the biggest guns and are the quickest to draw. These duels foster social contempt—even in the workplace—and they warp the electorate. And finally, the remedies that have been proposed don’t seem to holster many weapons; in fact, they add bullets to the chamber in some cases. Marietta and Barker’s pessimistic conclusions will challenge idealistic reformers.
Banned Emotions
Authors: Otis Laura 
Published: April 2019

Abstract
Who benefits, and who loses, when emotions are described in particular ways? How can metaphors such as “hold on” and “let go” affect people’s emotional experiences? Banned Emotions draws on the latest research in neuroscience and psychology to challenge popular ideas about emotions that should supposedly be suppressed. This interdisciplinary book breaks taboos by exploring emotions in which people are said to “indulge”: self-pity, prolonged crying, chronic anger, grudge-bearing, bitterness, and spite. By focusing on metaphors for these emotions in classic novels, self-help books, and popular films, Banned Emotions exposes their cultural and religious roots. Examining works by Dante, Dickens, Dostoevsky, Kafka, Forster, and Woolf in parallel with Bridesmaids, Fatal Attraction, and Who Moved My Cheese?, Banned Emotions reveals patterns in the ways emotions are represented that can make people so ashamed of feelings, they may stifle emotions that they need to work through. By analyzing the ways that physiology and culture combine in emotion metaphors, Banned Emotions shows that emotion regulation is a political as well as a biological issue. Banned Emotions considers the emotions of women abandoned by their partners and asks whether the psychological “attachment” metaphor is the best way to describe human relationships. Recent studies of emotion regulation indicate that reappraisal works better than suppression, which over time can damage a person’s health. Socially discouraged emotions such as self-pity emerge from lived experiences, often the experiences of people who hold less social power. Emotion metaphors like “move on” deflect attention from the social problems that have inspired emotions to the individuals who feel them—people who need to think about their emotions and their causes in the world.
What Academics Really Want
Authors: Brennan Jason , Magness Phillip 
Published: April 2019

Abstract
This chapter discusses the basic incentives that faculty, students, and administrators face, especially at so-called R1 (doctoral-granting with the highest research activity) universities. Different people have somewhat different motivations. Some are more driven by fame and prestige, some by money, some by intellectual curiosity, some by love, and others by a desire to push their ideology. Different institutions also structure their incentives somewhat differently. The university is a political environment where different groups and individuals compete for power and resources. Thus, it is not that the university is full of gremlins or beset by poltergeists, but that individual professors, students, and administrators face incentives that put them in conflict with the core values of the university.
Why Most Academic Advertising Is Immoral Bullshit
Authors: Brennan Jason , Magness Phillip 
Published: April 2019

Abstract
This chapter criticizes how universities and colleges market themselves to potential students. In particular, it examines how they promise (or at least strongly insinuate) that they will transform students, teach them to think, and turn them into leaders. The problem is that very little evidence exists that universities succeed in doing any of these things. Thus, universities engage in, if not quite false advertising, what might instead be called negligent advertising. They are not exactly lying, but selling snake oil. There is no proof that universities deliver, or are capable of making good, on most of their promises. Universities do not just engage in unethical marketing. Rather, they seem to not even do much educating.
On Reading Entrails and Student Evaluations
Authors: Brennan Jason , Magness Phillip 
Published: April 2019

Abstract
In the United States, most universities and colleges ask students to complete course evaluations at the end of each semester. They ask students how much they’ve learned, how much they studied, whether the instructor seemed well-prepared, and how valuable the class was overall. This chapter examines how colleges routinely make faculty hiring, retention, and promotion decisions on the basis of what they ought to know are invalid tests. It argues that student course evaluations do not track teacher effectiveness. Using these as the bases of determining hires, promotions, tenure, or raises for faculty is roughly on par with reading entrails or tea leaves to make such decisions. The chapter also explains why universities continue to use student course evaluations.
Grades: Communication Breakdown
Authors: Brennan Jason , Magness Phillip 
Published: April 2019

Abstract
This chapter assesses how professors grade students. It argues that the practice of grading is replete with problems. Grades are a kind of language. They are meant to be a form of communication. They are sometimes meant to communicate to students how well they’ve mastered a set of material. Most colleges calculate grade point averages (GPAs) and compare students to one another. Grades are also sometimes meant to communicate to outsiders something about how good a student is, and how he or she compares to other students from other universities. However, the grading and GPA systems are such a mess that they largely fail to accomplish these goals. In some cases, the mathematics used to calculate an average final grade in a class are incoherent. In nearly all cases, the mathematics used to calculate students’ GPAs are also incoherent.