bluuebunny/crossref_metadata_2025 huggingface dataset:
Humor in Interpersonal Communication
Authors: Booth-Butterfield Melanie , Wanzer Melissa
Published: May 2018

Effective humor enactment has been proven to be beneficial to both senders and receivers of the communication. Use of humor in social interaction has the potential to elicit positive perceptions, improve interpersonal interactions, reduce conflict, aid in coping, and even facilitate health outcomes. In contrast, poorly communicated, ill-timed, or maladaptive humor is often detrimental to both personal perceptions and relationships. Specific factors regarding these bidirectional outcomes are examined in this article.

Humorous enactments are inherently a goal-oriented form of communication that involves social, cognitive, emotional, and behavioral elements. The individual intends to accomplish some goal through communicating humor, no matter how obscure or subconscious the act might seem. Hence the communicator encodes verbal and/or nonverbal messages to achieve this aim. By comparison, genuine responses to humor (whether a trait pattern or situationally immediate) are not goal-oriented, but rather spontaneous reactions to humorous messages. Therefore, laughter, snickering, and the like may be authentic, unguarded amusement responses.

Research and discussion of interpersonal humor entail several foundational premises which must be addressed: productive and unproductive forms of humor, differences between source and receiver approaches, interactional versus presentational perspectives, varying functions and outcomes of humor across different stages of relationship development and decline, as well as attention to some less-often studied contexts. The application of theoretical frameworks such as Incongruity, Instructional Humor Processing, Superiority, Dispositional, and Benign Violations theories help guide our predictions and explanations of humorous messages.
Don't Expose Yourself: Discretionary Exposure to Political Information
Authors: Sood Gaurav , Lelkes Yphtach
Published: May 2018

The news media have been disrupted. Broadcasting has given way to narrowcasting, editorial control to control by “friends” and personalization algorithms, and a few reputable producers to millions with shallower reputations. Today, not only is there a much broader variety of news, but there is also more of it. The news is also always on. And it is available almost everywhere. The search costs have come crashing down, so much so that much of the world’s information is at our fingertips. Google anything and the chances are that there will be multiple pages of relevant results.

Such a dramatic expansion of choice and access is generally considered a Pareto improvement. But the worry is that we have fashioned defeat from the bounty by choosing badly. The expansion in choice is blamed for both, increasing the “knowledge gap,” the gap between how much the politically interested and politically disinterested know about politics, and increasing partisan polarization. We reconsider the evidence for the claims. The claim about media’s role in rising knowledge gaps does not need explaining because knowledge gaps are not increasing. For polarization, the story is nuanced. Whatever evidence exists suggests that the effect is modest, but measuring long-term effects of a rapidly changing media landscape is hard and may explain the results.

As we also find, even describing trends in basic explanatory variables is hard. Current measures are beset with five broad problems. The first is conceptual errors. For instance, people frequently equate preference for information from partisan sources with a preference for congenial information. Second, survey measures of news consumption are heavily biased. Third, behavioral survey experimental measures are unreliable and inapt for learning how much information of a particular kind people consume in their real lives. Fourth, measures based on passive observation of behavior only capture a small (likely biased) set of the total information consumed by people. Fifth, content is often coded crudely—broad judgments are made about coarse units, eliding over important variation.

These measurement issues impede our ability to answer the extent to which people choose badly and the attendant consequences of such. Improving measures will do much to advance our ability to answer important questions.
Crime Prevention Through Environmental Design
Authors: Armitage Rachel
Published: May 2018

Crime Prevention Through Environmental Design (CPTED) is an approach to crime reduction that seeks to reduce perceived opportunities for crime through the design and management of the built or, less often, the natural environment. It is based on a set of principles, which can be applied as a guide to the design and construction of buildings, as well as the organization of spaces around them. Because CPTED provides a guide rather than a rigid specification, with a range of possible realizations, design compliance with its principles is often recognized through an award scheme, such as Secured by Design (SBD) in the United Kingdom and the Police Label Secured Housing in the Netherlands. Research has consistently demonstrated that CPTED is an effective crime reduction approach—reducing crime, alleviating the fear of crime, and enhancing feelings of safety. Its increasing recognition within planning policy reflects a growing acknowledgment of efficacy.
Prison History
Authors: Rubin Ashley T.
Published: May 2018

Prisons are government-sanctioned facilities designed for the long-term confinement of adults as punishment for serious offenses. This definition of prisons, frequently belied by actual practice but an accurate representation of the prison as an ideal type, emerged relatively late in human history. For most of Western history, incarceration played a minor role in punishment and was often reserved for elites or political offenders; however, it was rarely considered a punishment in its own right for most offenders. The notion of the prison as a place of punishment emerged gradually, according to most accounts, over the 17th through 19th centuries. Although there were several precursors to penal incarceration, the most influential was the 17th-century Dutch workhouse, the first formal uses of penal incarceration in a prison as a distinct institution began with the American proto-prison in late 18th century and evolved into the modern prison in the early to mid-19th century. These modern prisons proved influential around the world. In late-19th-century America, however, the modern prison experienced a series of re-imaginings or iterations beginning with a proliferation of different forms, including distinctive forms of Southern punishment (convict leasing, chain gangs, and plantation-style prisons), specialized prisons across the country (women’s prisons, adult reformatories, and maximum-security prisons), and efforts to reduce reliance on prisons (drawing on innovations from Australia and Ireland). This flurry of activity was followed by a period of serial re-creation in the 20th century in the form of the big-house prison, the correctional institution, and the warehouse prison, including its subtype: the supermaximum-security prison. In this recent period, American prisons have once again become models copied by other countries.
Protestant Christianity in Modern Korea
Authors: Kim Sean C.
Published: May 2018

Korea is the only Asian nation with a significant Protestant presence. One in five South Koreans professes the faith. With more than eight and a half million believers, Protestantism as an organized religion ranks second numerically, not far behind Buddhism, but in terms of power and influence, it is unrivalled. Protestants occupy a central position in the country’s politics, society, and culture. Western missionaries, mostly Americans, introduced Protestantism in the late 19th century. As bearers of Anglo-American civilization, the missionaries built not only churches but also modern hospitals and schools. Korean converts, however, quickly assumed leadership under a policy of self-propagation, self-government, and self-support. In the 1920s and 1930s, the church came of age under popular revivalists who commanded national audiences. The process of indigenization also involved the adaptation to local beliefs and practices, producing a distinctive Korean Protestant tradition. Moreover, because of Japanese colonization, Protestantism did not suffer the stigma of Western imperialism common in other mission fields. Many Protestants, in fact, became nationalist leaders. Following World War II, Korea suffered the division of the country and the Korean War. Protestantism was extinguished in the communist north, leading to a mass exodus to the south, but in South Korea, it thrived. Industrialization and urbanization provided opportunities for the churches to create a sense of community, but it was primarily the aggressive one-on-one proselytization and mass evangelistic campaigns that fueled the dramatic expansion. From the 1960s to 1980s, South Korea became the fastest-growing Christian population in the world. The growth stalled in the 1990s because of the church’s support for previous dictatorial regimes as well as scandals involving Protestant political and corporate leaders. Yet Protestantism today remains a vibrant force in South Korea, home to the largest churches in the world and the base for thousands of Korean missionaries.
Newspapers as Sources for African History
Authors: Hunter Emma
Published: May 2018

Newspapers have become increasingly important as a source for African history, and the range of historical questions newspapers have been employed to address has expanded dramatically. Newspapers are not only sources for political history, they also have much to teach us about the social, cultural, and intellectual history of Africa. They were spaces of literary and textual experimentation. They also played an important role in the creation of new identities. It is essential, however, that we approach newspapers critically as sources and think carefully about their limitations, as well as the opportunities they present to the historian.
Ethnicity in Africa
Authors: Lynch Gabrielle
Published: May 2018

Among today’s scholars there is a near consensus that precolonial African identities were relatively fluid, permeable, overlapping, and complex; that ethnic identities are socially constructed; and that a colonial order of delineated control encouraged Africans to rethink group identities and heightened a sense of socioeconomic and political competition along ethnic lines. There is also growing consensus that ethnic identities are nevertheless the subject of ongoing (re)negotiation and that, to find resonance, the politicization of ethnicity, while instrumental in motivation and opportunistic in character, must be rooted in linguistic, cultural, and socioeconomic similarities and communal experiences of marginalization, neglect, injustice, and achievement. Many scholars also emphasize how the realities of ethnically delineated political support reflect pragmatism and expectations of patronage in the context of difficult and unequal socioeconomic contexts, as well as the significance of remembered pasts and associated narratives of justice and strategies of acquisition. Such realities and discursive repertoires provide a list of grievances that elites can use to foster a sense of difference and mobilize local support bases, but that also provide nonelites with a means to question and counter intra- and intercommunal differences and thus social and spatial inequalities. Ethnic support then strengthened by a reinforcing cycle of ethnic bias and expectations of greater levels of assistance from co-ethnics. According to such arguments, ethnic identification and political support are rational, but not for the simple reasons that classic primordial, instrumental or neo-patrimonial accounts suggest.
Ismaili and Fatimid North Africa
Authors: Baker Christine D.
Published: May 2018

The Fatimid dynasty ruled North Africa from 909 to 1171 CE. The Fatimids identified as Isma’ili Shi’is and they declared a Shi’i countercaliphate in Qayrawan to rival the Sunni ‘Abbasids in Baghdad. Their dynasty rose to power from an underground missionary movement, but eventually conquered most of North Africa, the Levant, the Muslim holy cities of Mecca and Medina, and Yemen. Their first capital was in Qayrawan, but they are best known for founding the city of Cairo as their imperial capital in 969. The Fatimids linked North African and Mediterranean trade with the Indian Ocean via the Red Sea, creating an era of unprecedented economic growth. Further, Fatimid sponsorship of Isma’ili Shi’i ritual and scholarship allowed for the development of several Isma’ili movements that have persisted into the modern era. The Fatimid era ended in the 12th century during the rise of Turkic dynasties and the influx of Crusader forces into the eastern Mediterranean region.
Prisoners, Ransoms, and Slavery in the Maghrib
Authors: Hopley Russell
Published: May 2018

The topic of prisoners, ransoms, and slavery in the Maghrib (that is, the lands of the Islamic west—the area that today encompasses North Africa, and historically, also the regions of Iberia and Sicily that came under Muslim rule) is of considerable chronological and geographical scope extending from the earliest establishment of Islamic rule in the region during the second half of the 7th century, persisting to the final decades of the 20th century, and enslaving or otherwise taking prisoner peoples from areas as geographically diverse as West Africa, the southern coastal regions of Europe, and as far north as Ireland and Iceland. The practice of slavery and the taking of prisoners in the Maghrib are thus of substantial historical significance. Yet, it is only in comparatively recent times that this complex topic has drawn the attention of scholars. Therefore, our understanding of slavery and the taking of prisoners in the Maghrib, especially during the medieval period, remains in its incipience.
Naikan: A Meditation Method and Psychotherapy
Authors: Chilson Clark
Published: May 2018

“Naikan” 内観 is a self-reflective form of meditation founded by Yoshimoto Ishin 吉本伊信 (1916–1988), who developed it from a lay Shin Buddhist practice called mishirabe身調べ. After Yoshimoto used it to help prisoners in the 1950s, psychiatrists in the 1960s started to use it as a psychotherapy. Today in Japan it is the most popular psychotherapeutic method that originated in Buddhism.

Naikan involves self-reflection on three questions: What have I received from a significant other? What have I given back to that person? What troubles and difficulties did I cause that person? People doing Naikan ask themselves these questions in relation to a family member or some other person during particular times in their lives.

There are two types of the practice: intensive Naikan (shūchū naikan集中内観) and daily Naikan (nichijō naikan日常内観 or bunsan naikan分散内観). The former is done continually for a week at a Naikan training center, of which there are about twenty-five in Japan and several outside Japan in Austria, Germany, and the United States. During intensive Naikan, those doing Naikan report individually eight or so times a day their answers to the three questions to an “interviewer” (mensetsusha面接者). Daily Naikan is done as part of a person’s everyday normal routine for as short as a few minutes or as long as two hours a day. Intensive or daily Naikan is offered as a therapy at about twenty medical institutions in Japan and another fifteen in China.

Intensive Naikan is commonly done for one of four reasons. First, it is done to solve a specific problem, such as alcoholism, gambling addiction, a psychosomatic disorder, or a bad relationship with a family member. Second, it is used to train employees so they can interact better with customers and colleagues. The Toyoko Inn, for example, which has over 230 hotels throughout Japan, requires all its full-time employees to do intensive Naikan. Third, it cultivates greater self-awareness with regard to, for example, how our minds work. Finally, it is done to discover the true nature of our lives through a spiritual awakening, which commonly entails the realization of how we live due to the care of others and how we suffer because of our own self-centeredness. This final purpose is in accordance with Yoshimoto’s view of Naikan as a method for learning how to live happily regardless of one’s life circumstances. Those who do Naikan for non-psychotherapeutic purposes sometimes use the term “Naikanhō” 内観法 (Naikan method) to distinguish their aims from Naikan therapy (Naikan ryōhō) 内観療法, which is used to solve a particular problem. But regardless of whether Naikan is done for self-developmental, spiritual, or for therapeutic reasons, the Naikan method of reflecting on the three Naikan questions is the same.
Oscar Lewis, Urban Poverty, and The Children of Sánchez
Authors: Salyers Joshua K.
Published: May 2018

Revolutionary leaders favored depictions of Mexico City in the mid-20th century that highlighted the progress and orderly growth of a modern industrial city. The ruling party made Mexico City the focus of post–World War II development policies and the showcase for the success of those policies in achieving the new goals of the Mexican Revolution during a period of sustained economic growth known as the “Mexican miracle.” When, in the early 1960s, the American anthropologist Oscar Lewis published The Children of Sánchez, his popular study of urban poverty, and turned the public’s attention away from the sites that underscored the official narrative of orderly industrial growth, it incited a heated public debate in Mexico City. The book contained the oral histories of a family living in the low-income neighborhood of Tepito, in the center of the capital, and was a shocking account, told in their own words, of a family’s attempt to survive urban life. Supporters of the modernizing policies of federal officials and the capital’s mayor, Ernesto Uruchurtu, attacked the book in the press and even filed formal complaints with Mexico’s attorney general demanding that the book and its author be banned from the country and the publisher reprimanded. They claimed that the book was too vulgar for public consumption and called it a foreigner’s attack on the reputation of the country and the city. Critics of the Institutional Revolutionary Party used the publicity generated by the attacks to open up a dialog about the marginalized people left behind by urban development and engaged in the debates as a safe way to express its own concerns about Uruchurtu’s inhumane development policies and the government’s insistence on hiding reality to present the city to the international community as a modern showcase.
The Public Sphere in Mexico since the Mid-20th Century
Authors: Freije Vanessa
Published: May 2018

At midcentury, the expansion of a middle class, rapid urbanization, and rising literacy rates transformed Mexico’s public sphere. Available reading material and access to television expanded significantly, fostering the creation of new publics across the country. Civic associations and cultural centers also offered spaces of sociability where civil society contested the prevailing political culture. The 1960s and 1970s further witnessed mounting public protests, popular movements, and guerrilla warfare. During these decades, print media gradually voiced greater criticism of the ruling Partido Revolucionario Institucional (PRI), and regional journalists were often the most confrontational. In the decades since, the issues and voices represented by media have diversified, while journalists have also faced increased insecurity and violence.
The United States and the 1964 Brazilian Military Coup
Authors: Spektor Matias
Published: May 2018

The John F. Kennedy administration took a bet on the incoming president of Brazil, João Goulart, as he took office on September 8, 1961. Goulart was not a radical socialist, but his opponents portrayed him as an unpredictable nationalist who might unadvisedly fuel the flames of social upheaval and radical revolution, turning Brazil into a second Cuba. Yet, the White House estimated that Goulart was someone they could do business with and sympathized with the idea of Reformas de Base (Goulart’s program of “basic reforms”), which included the extension of labor protections to rural workers, redistributive agrarian reform, and universal suffrage. United States support for Goulart materialized in the form of economic aid, financial assistance via the IMF, and development assistance via the Alliance for Progress partnership. Within a year, however, the tide turned as Goulart failed to comply with American demands that he ban leftists from his cabinet. In a matter of months in 1962, the White House abandoned any hopes of engagement with the Brazilian president. While the crisis that led to Goulart’s fall in March 1964 was the making of domestic political actors within Brazil—as was the military coup to unseat the president—the likelihood and success rate of the golpe grew as the United States rolled out successive rounds of targeted actions against Goulart, including diplomatic and financial pressure, threats of abandonment, support for opposition politicians, collusion with coup plotters, signaling future military support for the plotters in the eventuality of civil war, and the granting of immediate diplomatic recognition for the incoming authoritarian military leaders after the coup. After Goulart, Brazil remained under authoritarian rule for two consecutive decades.
prices
Authors: Erdkamp Paul
Published: May 2018

While our sources mention numerous prices of a wide range of commodities, the question remains to what extent these prices offer insight into the ancient economy. Despite the wealth of data, reliable prices of everyday goods under normal market conditions are rare. The extent to which they can be used to analyze such topics as market integration, living standards, market stability, and inflation is limited. Only regarding Ptolemaic and Roman Egypt do we possess sufficient market prices (rather than imposed prices or valuations) to conduct meaningful analyses. For most of the rest of the empire, the prices—in particular those of everyday goods—are generally too uncertain, too sparse, and too diverse to form a solid basis for economic analysis. It is a valid question, moreover, to what extent prices in the ancient world reflect the interplay of supply and demand according to modern economic theory. Nevertheless, ancient writers depict price levels as depending on the interplay of supply and demand, and market transactions, as narrated in our sources, emphasizing competition and bargaining, make clear that price formation was largely determined by economic forces. Hence, prices fluctuated over time and differed in various places. The authorities tried to keep prices of staple foods low by influencing market conditions, but direct price fixing was rare.
Public Participation in Planning for Community Management of Natural Hazards
Authors: Sarzynski Andrea , Cavaliere Paolo
Published: May 2018

Public participation in environmental management, and more specifically in hazard mitigation planning, has received much attention from scholars and practitioners. A shift in perspective now sees the public as a fundamental player in decision-making rather than simply as the final recipient of a policy decision. Including the public in hazard mitigation planning brings widespread benefits. First, communities gain awareness of the risks they live with, and thus, this is an opportunity to empower communities and improve their resilience. Second, supported by a collaborative participation process, emergency managers and planners can achieve the ultimate goal of strong mitigation plans.

Although public participation is highly desired as an instrument to improve hazard mitigation planning, appropriate participation techniques are context dependent and some trade-offs exist in the process design (such as between representativeness and consensus building). Designing participation processes requires careful planning and an all-around consideration of the representativeness of stakeholders, timing, objectives, knowledge, and ultimately desired goals to achieve. Assessing participation also requires more consistent methods to facilitate policy learning from diverse experiences. New decision-support tools may be necessary to gain widespread participation from laypersons lacking technical knowledge of hazards and risks.
Real-Time Flash Flood Forecasting
Authors: Gourley Jonathan J. , Clark Robert A.
Published: May 2018

Flash floods are one of the world’s deadliest and costliest weather-related natural hazards. In the United States alone, they account for an average of approximately 80 fatalities per year. Damages to crops and infrastructure are particularly costly. In 2015 alone, flash floods accounted for over $2 billion of losses; this was nearly half the total cost of damage caused by all weather hazards. Flash floods can be either pluvial or fluvial, but their occurrence is primarily driven by intense rainfall. Predicting the specific locations and times of flash floods requires a multidisciplinary approach because the severity of the impact depends on meteorological factors, surface hydrologic preconditions and controls, spatial patterns of sensitive infrastructure, and the dynamics describing how society is using or occupying the infrastructure.

Real-time flash flood forecasting systems rely on the observations and/or forecasts of rainfall, preexisting soil moisture and river-stage states, and geomorphological characteristics of the land surface and subsurface. The design of the forecast systems varies across the world in terms of their forcing, methodology, forecast horizon, and temporal and spatial scales. Their diversity can be attributed at least partially to the availability of observing systems and numerical weather prediction models that provide information at relevant scales regarding the location, timing, and severity of impending flash floods. In the United States, the National Weather Service (NWS) has relied upon the flash flood guidance (FFG) approach for decades. This is an inverse method in which a hydrologic model is run under differing rainfall scenarios until flooding conditions are reached. Forecasters then monitor observations and forecasts of rainfall and issue warnings to the public and local emergency management communities when the rainfall amounts approach or exceed FFG thresholds. This technique has been expanded to other countries throughout the world. Another approach, used in Europe, relies on model forecasts of heavy rainfall, where anomalous conditions are identified through comparison of the forecast cumulative rainfall (in space and time) with a 20-year archive of prior forecasts. Finally, explicit forecasts of flash flooding are generated in real time across the United States based on estimates of rainfall from a national network of weather radar systems.
Early History of Animal Domestication in Southwest Asia
Authors: Arbuckle Benjamin S.
Published: May 2018

The domestication of livestock animals has long been recognized as one of the most important and influential events in human prehistory and has been the subject of scholarly inquiry for centuries. Modern understandings of this important transition place it within the context of the origins of food production in the so-called Neolithic Revolution, where it is particularly well documented in southwest Asia. Here, a combination of archaeofaunal, isotopic, and DNA evidence suggests that sheep, goat, cattle, and pigs were first domesticated over a period of several millennia within sedentary communities practicing intensive cultivation beginning at the Pleistocene–Holocene transition. Resulting from more than a century of data collection, our understanding of the chronological and geographic features of the transition from hunting to herding indicate that the 9th millennium bce and the region of the northern Levant played crucial roles in livestock domestication. However, many questions remain concerning the nature of the earliest predomestic animal management strategies, the role of multiple regional traditions of animal management in the emergence of livestock, and the motivations behind the slow spread of integrated livestock husbandry systems, including all four domestic livestock species that become widespread throughout southwest Asia only at the end of the Neolithic period.
Physical Properties of Silicone Gel Breast Implants
Authors: Jewell Mark L , Bengtson Bradley P , Smither Kate , Nuti Gina , Perry TracyAnn
Published: April 2018

Background

Surgical applications using breast implants are individualized operations to fill and shape the breast. Physical properties beyond shape, size, and surface texture are important considerations during implant selection.

Objectives

Compare form stability, gel material properties, and shell thickness of textured shaped, textured round, and smooth round breast implants from 4 manufacturers: Allergan, Mentor, Sientra, and Establishment Labs, through bench testing.

Methods

Using a mandrel height gauge, form stability was measured by retention of dimensions on device movement from a horizontal to vertical supported orientation. Dynamic response of the gel material (gel cohesivity, resistance to gel deformation, energy absorption) was measured using a synchronized target laser following application of graded negative pressure. Shell thickness was measured using digital thickness gauge calipers.

Results

Form stability, gel material properties, and shell thickness differed across breast implants. Of textured shaped devices, Allergan Natrelle 410 exhibited greater form stability than Mentor MemoryShape and Sientra Shaped implants. Allergan Inspira round implants containing TruForm 3 gel had greater form stability, higher gel cohesivity, greater resistance to gel deformation, and lower energy absorption than those containing TruForm 2 gel and in turn, implants containing TruForm 1 gel. Shell thickness was greater for textured vs smooth devices, and differed across styles.

Conclusions

Gel cohesivity, resistance to gel deformation, and energy absorption are directly related to form stability, which in turn determines shape retention. These characteristics provide information to aid surgeons choosing an implant based on surgical application, patient tissue characteristics, and desired outcome.
Base-pair resolution detection of transcription factor binding site by deep deconvolutional network
Authors: Salekin Sirajul , Zhang Jianqiu Michelle , Huang Yufei
Published: May 2018

Motivation

Transcription factor (TF) binds to the promoter region of a gene to control gene expression. Identifying precise TF binding sites (TFBSs) is essential for understanding the detailed mechanisms of TF-mediated gene regulation. However, there is a shortage of computational approach that can deliver single base pair resolution prediction of TFBS.

Results

In this paper, we propose DeepSNR, a Deep Learning algorithm for predicting TF binding location at Single Nucleotide Resolution de novo from DNA sequence. DeepSNR adopts a novel deconvolutional network (deconvNet) model and is inspired by the similarity to image segmentation by deconvNet. The proposed deconvNet architecture is constructed on top of ‘DeepBind’ and we trained the entire model using TF-specific data from ChIP-exonuclease (ChIP-exo) experiments. DeepSNR has been shown to outperform motif search–based methods for several evaluation metrics. We have also demonstrated the usefulness of DeepSNR in the regulatory analysis of TFBS as well as in improving the TFBS prediction specificity using ChIP-seq data.

Availability and implementation

DeepSNR is available open source in the GitHub repository (https://github.com/sirajulsalekin/DeepSNR)

Supplementary information

Supplementary data are available at Bioinformatics online.
Two C++ libraries for counting trees on a phylogenetic terrace
Authors: Biczok R , Bozsoky P , Eisenmann P , Ernst J , Ribizel T , Scholz F , Trefzer A , Weber F , Hamann M , Stamatakis A
Published: May 2018

Motivation

The presence of terraces in phylogenetic tree space, i.e. a potentially large number of distinct tree topologies that have exactly the same analytical likelihood score, was first described by Sanderson et al. However, popular software tools for maximum likelihood and Bayesian phylogenetic inference do not yet routinely report, if inferred phylogenies reside on a terrace, or not. We believe, this is due to the lack of an efficient library to (i) determine if a tree resides on a terrace, (ii) calculate how many trees reside on a terrace and (iii) enumerate all trees on a terrace.

Results

In our bioinformatics practical that is set up as a programming contest we developed two efficient and independent C++ implementations of the SUPERB algorithm by Constantinescu and Sankoff (1995) for counting and enumerating trees on a terrace. Both implementations yield exactly the same results, are more than one order of magnitude faster, and require one order of magnitude less memory than a previous thirrd party python implementation.

Availability and implementation

The source codes are available under GNU GPL at https://github.com/terraphast.

Supplementary information

Supplementary data are available at Bioinformatics online.
Repeat Syphilis Is More Likely to Be Asymptomatic in HIV-Infected Individuals: A Retrospective Cohort Analysis With Important Implications for Screening
Authors: Kenyon Chris , Osbak Kara Krista , Apers Ludwig
Published: April 2018

There is conflicting evidence as to whether repeat syphilis is more likely to present asymptomatically than initial syphilis. If it is, then this would motivate more frequent and long-term syphilis screening in persons with a history of multiple episodes of syphilis. We conducted detailed folder reviews of all individuals with 4 or more diagnoses of syphilis between 2000 and 2017 at the Institute of Tropical Medicine, Antwerp, and assessed if there was a difference in the proportion presenting with symptomatic (primary and secondary) vs asymptomatic (latent) syphilis in initial vs repeat syphilis. Forty-five clients with 4 or more episodes of syphilis were included in the study. All were HIV-infected. Repeat episodes of syphilis were less likely to be symptomatic than initial episodes (35/160 [21.9%] vs 28/45 [62.2%]; P < .001). Frequent screening in those with HIV infection may be the only way to diagnose repeat episodes of syphilis. Care providers can use this information to motivate persons with multiple episodes of syphilis to be screened every 3 to 6 months.
Prevalence and Genetic Diversity of Grabloviruses in Free-Living Vitis spp.
Authors: Cieniewicz Elizabeth , Thompson Jeremy R. , McLane Heather , Perry Keith L. , Dangl Gerald S. , Corbett Quinlan , Martinson Timothy , Wise Alice , Wallis Anna , O’Connell James , Dunst Rick , Cox Kerik , Fuchs Marc
Published: May 2018

The distribution and diversity of grapevine red blotch virus (GRBV) and wild Vitis virus 1 (WVV1) (genus Grablovirus; family Geminiviridae) were determined in free-living Vitis spp. in northern California and New York from 2013 to 2017. Grabloviruses were detected by polymerase chain reaction in 28% (57 of 203) of samples from California but in none of the 163 samples from New York. The incidence of GRBV in free-living vines was significantly higher in samples from California counties with high compared with low grape production (χ2 = 83.09; P < 0.001), and in samples near (<5 km) to compared with far (>5 km) from vineyards (χ2 = 57.58; P < 0.001). These results suggested a directional spread of GRBV inoculum predominantly from vineyards to free-living Vitis spp. WVV1 incidence was also significantly higher in areas with higher grape production acreage (χ2 = 16.02; P < 0.001). However, in contrast to GRBV, no differential distribution of WVV1 incidence was observed with regard to distance from vineyards (χ2 = 0.88; P = 0.3513). Two distinct phylogenetic clades were identified for both GRBV and WVV1 isolates from free-living Vitis spp., although the nucleotide sequence variability of the genomic diversity fragment was higher for WWV1 (94.3 to 99.8% sequence identity within clade 1 isolates and 90.1 to 100% within clade 2 isolates) than GRBV (98.3% between clade 1 isolates and 96.9 to 100% within clade 2 isolates). Additionally, evidence for intraspecific recombination events was found in WVV1 isolates and confirmed in GRBV isolates. The prevalence of grabloviruses in California free-living vines highlights the need for vigilance regarding potential grablovirus inoculum sources in order to protect new vineyard plantings and foundation stock vineyards in California.
Visceral Fat Is Associated With Mucosal Healing of Infliximab Treatment in Crohn’s Disease
Authors: Shen Weisong , Cao Lei , Li Yi , Cai Xingchen , Ge Yuanyuan , Zhu Weiming
Published: May 2018

BACKGROUND:

Visceral fat is the pathogenesis of Crohn’s disease and is associated with disease status.

OBJECTIVE:

This study aimed to evaluate the effect of the visceral fat on mucosal healing in patients with Crohn’s disease after infliximab induction therapy

DESIGN:

This was a retrospective study.

SETTINGS:

The study was conducted in a tertiary referral hospital.

PATIENTS:

Between 2011 and 2017, 97 patients with Crohn’s disease with the presence of ulcers underwent infliximab therapy.

MAIN OUTCOME MEASURES:

We studied them retrospectively. Mucosal healing was the end point. Patients composed 2 groups: mucosal healing and no mucosal healing. Univariate, multivariate, and receiver operating characteristic curve analyses determined the predictive value of the visceral fat area.

RESULTS:

Univariate analysis showed a statistically significant difference in the smoking history between the groups. Mucosal healing rates after infliximab were lower among active smokers (p = 0.022). Healed patients had significantly less visceral fat area before therapy (47.76 ± 4.94 vs 75.88 ± 5.55; p = 0.000) and a lower mesenteric fat index (0.52 ± 0.04 vs 0.89 ± 0.07; p = 0.000). There was no significant difference in the subcutaneous fat area (87.39 ± 5.01 vs 93.31 ± 6.95; p = 0.500). Multivariate analysis showed that only visceral fat area (OR = 0.978 (95% CI, 0.964–0.992); p = 0.002) and smoking history (OR = 0.305 (95% CI, 0.089–0.996); p = 0.041) were independent factors for mucosal healing. Receiver operating characteristic curve analysis showed predictive cutoff values of 61.5 cm2 and 0.62 for visceral fat area and mesenteric fat index.

LIMITATIONS:

This was a retrospective study.

CONCLUSIONS:

There was an association between increased visceral fat area and attenuated mucosal healing after infliximab therapy in biologically naive patients with Crohn’s disease, indicating a need for earlier increased infliximab doses among patients with increased visceral fat. See Video Abstract at http://links.lww.com/DCR/A590.
Using Endoscopic Submucosal Dissection as a Routine Component of the Standard Treatment Strategy for Large and Complex Colorectal Lesions in a Western Tertiary Referral Unit
Authors: Emmanuel Andrew , Gulati Shraddha , Burt Margaret , Hayee Bu’Hussain , Haji Amyn
Published: May 2018

BACKGROUND:

Colorectal endoscopic submucosal dissection results in high rates of en bloc resection, few recurrences, and accurate diagnosis, and it is useful in lesions with significant fibrosis. However, endoscopic submucosal dissection has not been widely adopted by Western endoscopists and the published experience from Western centers is very limited.

OBJECTIVES:

This study aims to report the outcomes from a UK tertiary center using colorectal endoscopic submucosal dissection as part of a standard lesion specific treatment approach.

DESIGN:

This was a retrospective study.

SETTING:

The study was conducted in a tertiary referral unit for interventional endoscopy in the United Kingdom.

PATIENTS:

A total of 116 colorectal lesions were resected using endoscopic submucosal dissection or hybrid endoscopic submucosal dissection in 107 patients.

MAIN OUTCOME MEASURES:

Outcomes included complications, recurrence, requirement for surgery, en bloc and R0 resection.

RESULTS:

One hundred sixteen lesions (mean size 58.8mm) were resected using endoscopic submucosal dissection (n = 58) and hybrid endoscopic submucosal dissection (n = 58). Eighty-two (70.7%) had failed attempts at resection (n = 58) or extensive sampling before referral. Twelve contained invasive adenocarcinoma; endoscopic resection was curative in 6. Only 2 of 6 patients with noncurative endoscopic resection agreed to surgery, and none had lymph node metastases. Six of 7 perforations were successfully treated with endoscopic clips. Where endoscopic submucosal dissection was used alone, en bloc resection was achieved in 93% and R0 resection was achieved in 91%. Two patients experienced recurrence; both were managed with endoscopic resection.

LIMITATIONS:

This was a retrospective study. Procedures were planned as endoscopic submucosal dissection, but some may have been converted to hybrid endoscopic submucosal dissection and not recorded.

CONCLUSION:

Colorectal endoscopic submucosal dissection can be used in a Western center as part of a standard lesion-specific approach to deliver effective organ-conserving treatment to patients with large challenging lesions. Lesion assessment in Western practice should be improved to reduce the incidence of prior heavy manipulation and to guide appropriate referral. See Video Abstract at http://links.lww.com/DCR/A601.
Microcapsule Technology for Controlled Growth Factor Release in Musculoskeletal Tissue Engineering
Authors: Della Porta Giovanna , Ciardulli Maria C. , Maffulli Nicola
Published: May 2018

Tissue engineering strategies have relied on engineered 3-dimensional (3D) scaffolds to provide architectural templates that can mimic the native cell environment. Among the several technologies proposed for the fabrication of 3D scaffold, that can be attractive for stem cell cultivation and differentiation, moulding or bioplotting of hydrogels allow the stratification of layers loaded with cells and with specific additives to obtain a predefined microstructural organization. Particularly with bioplotting technology, living cells, named bio-ink, and additives, such as biopolymer microdevices/nanodevices for the controlled delivery of growth factors or biosignals, can be organized spatially into a predesigned 3D pattern by automated fabrication with computer-aided digital files. The technologies for biopolymer microcarrier/nanocarrier fabrication can be strategic to provide a controlled spatiotemporal delivery of specific biosignals within a microenvironment that can better or faster address the stem cells loaded within it. In this review, some examples of growth factor–controlled delivery by biopolymer microdevices/nanodevices embedded within 3D hydrogel scaffolds will be described, to achieve a bioengineered 3D interactive microenvironment for stem cell differentiation. Conventional and recently proposed technologies for biopolymer microcapsule fabrication for controlled delivery over several days will also be illustrated and critically discussed.
PRP as an Adjunct to Rotator Cuff Tendon Repair
Authors: Barber F. Alan
Published: May 2018

Arthroscopic rotator cuff repair is a commonly performed repair. Technical developments provide surgeons the tools to create biomechanically robust repairs. How can the biological response mirror the strong and stable surgery? Platelet-rich plasma (PRP) is a supraphysiological platelet concentration which may positively augment rotator cuff healing. Not all PRPs are the same. High leukocyte levels and thrombin activation may be detrimental to tendon healing. Thrombin activation triggers an immediate release of growth factors and may actually inhibit some parts of the healing response. Clear differences exist between liquid PRP (products released within hours after activation) and solid fibrin PRP which slowly releases factors over days. The heterogenicity data and grouping liquid and solid PRP together make systematic reviews confusing. Solid PRP fibrin constructs are often associated with increased tendon healing. PRP fibrin matrix offers the greatest promise for improving clinical success after rotator cuff tendon repair.
Combination attenuation offers strategy for live-attenuated coronavirus vaccines
Authors: Menachery Vineet D. , Gralinski Lisa E. , Mitchell Hugh D. , Dinnon Kenneth H. , Leist Sarah R. , Yount Boyd L. , McAnarney Eileen T. , Graham Rachel L. , Waters Katrina M. , Baric Ralph S.
Published: April 2018

With an ongoing threat posed by circulating zoonotic strains, new strategies are required to prepare for the next emergent coronavirus (CoV). Previously, groups had targeted conserved coronavirus proteins as a strategy to generate live-attenuated vaccine strains against current and future CoVs. With this in mind, we explored whether manipulation of CoV NSP16, a conserved 2’O methyltransferase (MTase), could provide a broad attenuation platform against future emergent strains. Using the SARS-CoV mouse model, a NSP16 mutant vaccine was evaluated for protection from heterologous challenge, efficacy in the aging host, and potential for reversion to pathogenesis. Despite some success, concerns for virulence in the aged and potential for reversion makes targeting NSP16 alone an untenable approach. However, combining a 2’O MTase mutation with a previously described CoV fidelity mutant produced a vaccine strain capable of protection from heterologous virus challenge, efficacy in aged mice, and no evidence for reversion. Together, the results indicate that targeting the CoV 2’O MTase in parallel with other conserved attenuating mutations may provide a platform strategy for rapidly generating live-attenuated coronavirus vaccines.

Significance

Emergent coronaviruses remain a significant threat to global public health and rapid response vaccine platforms are needed to stem future outbreaks. However, failure of many previous CoV vaccine formulations has clearly highlighted the need to test efficacy under different conditions and especially in vulnerable populations like the aged and immune-compromised. This study illustrates that despite success in young models, the NSP16 mutant carries too much risk for pathogenesis and reversion in vulnerable models to be used as a stand-alone vaccine strategy. Importantly, the NSP16 mutation can be paired with other attenuating approaches to provide robust protection from heterologous challenge and in vulnerable populations. Coupled with increased safety and reduced pathogenesis, the study highlights the potential for NSP16 attenuation as a major component of future live-attenuated coronavirus vaccines.