bluuebunny/crossref_metadata_2025 huggingface dataset:
Judgment and Decision Making in Teams
Authors: Park Guihyun , Hinsz Verlin B.
Published: October 2019

As organizations increasingly adopt team-based systems, team judgment and decision making are often preferred ways of making decisions compared to individual decision making. Teams are considered to have a greater potential to make a higher quality decision compared to individuals because teams can utilize a larger pool of information, team members can correct each other’s error, and team discussion can facilitate team processes that enhance team outcomes such as learning. Team judgment and decision making, however, are known to be subject to potential pitfalls such as polarization, common knowledge bias, and conformity pressures. This article summarizes team judgment and decision making from an information processing perspective in which information distributed among team members and interaction dynamics among team members (i.e., discussion, deliberation) determine the mechanisms whereby distributed information is expressed and elaborated and whereby it influences the ultimate team decision or judgment as discussed in The Emerging Conceptualization of Groups as Information Processors. Accordingly, studies on team judgment and decision making focus on processes whereby team members reach a team decision or judgment and the different factors that could make the team processes more effective. The current review attempts to achieve a balance in emphasis by including topics that are of interest both to academics as well as to practitioners of team judgment and decision making.
Biometric Technologies
Authors: Nguyen Nicole , Kaufman Emily
Published: October 2019

Since the turn of the 21st century, scholars have examined the technological advances and associated social implications related to the measurement and analysis of unique biological characteristics such as hand geometry and fingerprints, otherwise known as biometrics. Leading scientific journals like IET Biometrics have explored the scientific understandings and practical applications of biometric devices, such as the introduction of facial recognition technology into mass-market cell phones. Social science publications such as Surveillance & Society have investigated the social norms that inform the making of biometric technologies and their impacts on society. More specifically, these analyses have assessed the racialized, gendered, ableist, and classed contours of these emerging technologies that use the body as a metric. In fact, the earliest critical examinations of biometrics by scholars like Lyon and Pugliese focused on how normative understandings calibrated these emerging technologies to the white, able-bodied, cisgendered male body. Although additional scholars like Graham and Wood have demonstrated how digitizing surveillance through biometrics and other technologies intentionally has reinforced social inequities, they often fail to engage in analyses of race and gender. Since then, many scholars, especially women and women of color, have undertaken the study of biometrics to better understand how these technologies reinscribe power in global contexts. To do so, these scholars have added important historical, theoretical, and empirical insights that better account for how race, class, gender, ability, and other axes of social difference shape, and are shaped by, biometric technologies and their implementation. By examining the latest developments in biometrics and the aims of these technological innovations in India, Iraq, Mexico, Norway, the United States, and elsewhere, these scholars highlight and respond to critical absences in more conventional investigations of biometrics, which often ignore how power is enacted in and through these technologies. Browne’s extensive research, for example, has connected early practices of biometric branding to facilitate the transatlantic slave trade to contemporary biometric security practices in airports infused with gendered anti-Blackness. Other critical analyses examine the use of biometrics to police the poor, reinforce gender norms, pathologize disabled bodies, and regulate mobility from the diverse perspectives of those who design, implement, and experience these security practices. Through an exploration of the motivations, funding sources, and purposes of developing biometric technologies, this work takes seriously how biometrics are imbricated in the (re)constitution of power, (re)making of social difference, (re)articulation of spatialized power relations, and embodied experiences that often generate violence, anxiety, and dis-ease. In this bibliography, we organize these contributions around the who, what, where, when, why, and how of biometric systems.
Neurotuberculosis: Control of Steroid-Refractory Paradoxical Inflammatory Reaction With Ruxolitinib
Authors: Xie Yingda L , Ita-Nagy Fanny , Chen Ray Y , Manion Maura M , Sereti Irini , Pei Luxin , Holland Steven M
Published: October 2019

Paradoxical inflammatory reactions associated with treatment of neurotuberculosis can lead to severe morbidity and mortality and may not be controlled by steroids alone. We report the use of the Janus kinase inhibitor ruxolitinib to treat a steroid-refractory neurotuberculosis paradoxical reaction.
Balloon-Mounted Stents for Treatment of Refractory Flow Diverting Device Wall Malapposition
Authors: Cherian Jacob , Dabagh Mahsa , Srinivasan Visish M , Chen Stephen , Johnson Jeremiah , Wakhloo Ajay , Gupta Vipul , Macho J , Randles Amanda , Kan Peter
Published: October 2019

BACKGROUND

As indications for flow diversion (FD) have expanded, new challenges in deployment of flow diverting devices (FDDs) have been encountered. We present 4 cases with aneurysms in which deployment of FDDs were complicated by device malapposition and compromised opening in regions of parent vessel stenosis. In all 4 cases, a balloon-mounted stent was ultimately deployed within the FDD.

OBJECTIVE

To describe the use of balloon-mounted stents (BMS) within FDDs for correction of flow-limiting stenosis and device malapposition.

METHODS

Patients undergoing FD for treatment of aneurysms complicated by refractory flow-limiting stenosis were identified through multi-center retrospective review. Those cases requiring use of BMS were identified. Further investigation in one of the cases was performed with a simulated pulsatile blood flow model.

RESULTS

After attempts to perform balloon angioplasty proved unsuccessful, BMS deployment successfully opened the stenotic parent artery and improved FDD wall apposition in all 4 cases. Simulated pulsatile blood flow modeling confirmed improvements in the distribution of velocity, wall shear stress, oscillatory shear index, and flow pattern structure after stent deployment. One case was complicated by asymptomatic in-stent thrombosis.

CONCLUSION

In cases of FDD deployment complicated by flow-limiting stenosis refractory to conventional techniques, a BMS deployed within the FD can provide radial support to open both the stenotic device and parent artery. Resulting improvements in device wall apposition may portend greater long-term efficacy of FD. In-stent occlusion can occur and may reflect a thrombogenic interaction between the devices.
Can Digitization of Health Care Help Low-Resourced Countries Provide Better Community-Based Rehabilitation Services?
Authors: Balikuddembe Joseph Kimuli , Reinhardt Jan D
Published: October 2019

In the wake of globalization, proliferation of digital technologies (DTs) is rapidly changing many activities across sectors, including influencing health to “go digital.” Harnessing opportunities of DTs can be a pathway for delivery of health services, such as community-based rehabilitation (CBR) to the vulnerable groups of populations, particularly those in countries with low resources where health systems are weak and experiencing a deficit of trained health workers necessary to effectively deliver a full spectrum of health services. This perspective explored how some DTs can be leveraged in delivery of CBR services in rural and remote areas of countries with low resources. This is described based on information access and exchange, social satisfaction, shortages of rehabilitation workforce, professional development, and capacity building. However, since seizing advantages of DTs can inevitably be associated with spillovers and limitations, including needs prioritization, skills and language limitations, internet addiction and censorship issues, professionalism and ethical dilemmas, and sustainability, if proper measures are not taken, a caution is made. Moreover, as DTs are revolutionizing various activities across sectors, including health, this is not meant as a substitute for traditional health care activities, including those delivered through CBR, but rather to augment their delivery in settings with low resources and elsewhere.
EVALUATION OF RADIATION DOSE IN DIFFERENT POSITIONS AROUND THE PATIENT TABLE DURING INTERVENTIONAL CARDIOLOGY PROJECTIONS
Authors: Lahfi Y , Ismail A
Published: October 2019

The aim of the present study was to evaluate the radiation exposure around the patient table as relative to the cardiologist position dose value. The dose rates at eight points presuming staff positions were measured for PA, LAO 30° and RAO 30° radiographic projections, and then normalized to the cardiologist’s position dose-rate value. The results show that in PA and RAO 30° projections, the normalized dose rate was higher by 9–22% at the right side of the table at a distance of 50 cm, while it was higher up to 31% at the left side for the same measured points in the LAO 30°. The differences of normalized dose rates for the both table sides were lower and decreased at farther positions. The obtained results correspond to the recommendations of staff radiation protection in Cath-labs with regards to X-ray tube and detector positions.
Mutations and Overexpression of CYP51 Associated with DMI-Resistance in Colletotrichum gloeosporioides from Chili
Authors: Wei Ling-ling , Chen Wen-chan , Zhao Wei-cheng , Wang Jin , Wang Bing-ran , Li Feng-jie , Wei Meng-di , Guo Jun , Chen Chang-jun , Zheng Jia-qiu , Wang Kai
Published: October 2019

Chili anthracnose caused by Colletotrichum spp. is an annual production concern for growers in China. Sterol C14-demethylation inhibitors (DMIs, such as tebuconazole) have been widely used to control this disease for more than three decades. In the current study, of 48 isolates collected from commercial chili farms in Jiangsu Province of China during 2018 and 2019, 8 single-spore isolates were identified as Colletotrichum gloeosporioides and the rest were identified as C. acutatum. To determine whether the DMI resistance of isolates develops in the field, mycelial growth of the 48 isolates was measured in culture medium with and without tebuconazole. In all, 6 of the 8 C. gloeosporioides isolates were resistant to tebuconazole, but all 40 of the C. acutatum isolates were sensitive to tebuconazole. The fitness cost of resistance was low based on a comparison of fitness parameters between the sensitive and resistant isolates of C. gloeosporioides. Positive cross-resistance was observed between tebuconazole and difenconazole or propiconazole, but not prochloraz. Alignment results of the CgCYP51 amino acid sequences from the sensitive and resistant isolates indicated that mutations can be divided into three genotypes. Genotype I possessed four substitutions (V18F, L58V, S175P, and P341A) at the CgCYP51A gene but no substitutions at CgCYP51B, while genotype II had five substitutions (L58V, S175P, A340S, T379A, and N476T) at CgCYP51A, concomitant with three substitutions (D121N, T132A, and F391Y) at CgCYP51B. In addition, genotype III contained two substitutions (L58V and S175P) at CgCYP51A, concomitant with one substitution (T262A) at CgCYP51B. Molecular docking models illustrated that the affinity of tebuconazole to the binding site of the CgCYP51 protein from the resistant isolates was decreased when compared with binding site affinity of the sensitive isolates. Our findings provide not only novel insights into understanding the resistance mechanism to DMIs, but also some important references for resistance management of C. gloeosporioides on chili.
Physical characteristics and properties of estradiol softgel vaginal inserts
Authors: Simon James A. , Pickar James H. , Shadiack Annette M. , Warrier Bharat , Graham Shelli , Bernick Brian , Mirkin Sebastian
Published: October 2019

Objective:

TX-004HR is a low-dose estradiol (E2) softgel vaginal insert designed to be rapidly dissolving and mucoadhesive. This report describes the physical attributes and pharmacokinetic parameters of the softgel vaginal insert evaluated for the treatment of moderate to severe dyspareunia due to menopausal vulvar and vaginal atrophy.

Methods:

In vitro dissolution studies with 25-μg E2 inserts were performed and media samples were analyzed for E2 by high-performance liquid chromatography. Effects of body position on E2 bioavailability were assessed in a phase 1, randomized trial of the 25-μg softgel capsule versus a reference product in which women remained supine after dosing (n = 16), and in a substudy (n = 16) in which women were ambulatory or seated after dosing. Estradiol C
max, AUC0-24, and t
max were measured by high-performance liquid chromatography-tandem mass spectroscopy. A phase 2, randomized study (n = 50) of 10-μg E2 versus placebo inserts assessed timing of capsule disintegration at days 1 and 15.

Results:

In vitro testing detected more than 80% of E2 in the dissolution medium by 15 minutes (first time point measured). In the phase 1 studies, baseline-corrected E2 plasma levels were not significantly different regardless of supine versus ambulatory/seated position after dosing: C
max, 24.1 versus 34.3 pg/mL; AUC0-24, 77.6 versus 93.7 h · pg/mL; and t
max, 2.1 versus 1.9 hours, respectively. In the phase 2 study, no remnants of the softgel capsule were found at day 1 (6 hours) after dosing and day 15. Vaginal discharge was minimal (1/48 women; 2.1%).

Conclusions:

The presented data support rapid dissolution of the softgel capsule and similar E2 pharmacokinetic parameters regardless of body position after dosing.
Duration of reproductive years and time since menopause were associated with metabolic syndrome in postmenopausal parous women of Chinese ancestry
Authors: Yu Weihui , Hu Xiang , Yang Lijuan , Pan Wei , Deng Huihui , Chen Xiong , Zhou Qi , Chen Shuoping , Si Qiya , Chen Xueqin , Li Qianqian , Shen Feixia , Gu Xuejiang
Published: October 2019

Objective:

Although duration of reproductive years and time since menopause were previously implicated in the metabolic syndrome, the evidence is more limited. Few of the previous studies were able to take into account related reproductive variables simultaneously. The aim of the present study was to explore the influence of these two reproductive factors on the prevalence of metabolic syndrome in postmenopausal parous women from Southeast China.

Methods:

In all, 1,536 postmenopausal parous women were recruited. Self-reported information about reproductive status, including age at menarche, age at menopause, number of children, prepregnancy body weight, and oral contraceptive use, was collected, and duration of reproductive years and time since menopause were calculated. Clinical parameters related with metabolic syndrome were also measured.

Results:

Longer duration of reproductive years was significantly related with increased presence of the metabolic syndrome (odds ratio [OR] 1.570, 95% confidence interval [CI] 1.091, 2.259 for tertile 2 group; OR 1.850, 95% CI 1.163, 2.944 for tertile 3 group; P for trend = 0.010). Women with more than 20 years since menopause were more likely to experience metabolic syndrome (OR 2.422, 95% CI 1.109, 5.286, P = 0.026) and elevated blood pressure (OR 3.239, 95% CI 1.406, 7.458, P = 0.006) when compared with those with less than 10 years since menopause.

Conclusions:

Longer duration of reproductive years and time since menopause were associated with higher prevalence of metabolic syndrome in postmenopausal parous women from Southeast China.
Genetic polymorphisms in collagen-related genes are associated with pelvic organ prolapse
Authors: Li Lei , Sun Zhijing , Chen Juan , Zhang Ye , Shi Honghui , Zhu Lan
Published: October 2019

Objective:

Pelvic organ prolapse (POP) is a common health issue that has a profound negative influence on women's quality of life. Genetic susceptibility to POP has been increasingly investigated. In this study, we assessed the single-nucleotide polymorphisms (SNPs) of six collagen-related genes (COL14A1, COL5A1, COL4A2, COL3A1, COL1A1, and COL18A1) and the genetic association with POP in Chinese women.

Methods:

We performed a candidate gene association study of case women (n = 48) with stage III and IV prolapse and control women (n = 48) without prolapse. A target region sequencing approach was used to identify the SNPs in collagen-related genes. The association between SNPs and POP was examined by Fisher exact tests for unadjusted model and logistic regression analysis adjusted for delivery and pregnancy.

Results:

There was a significant association between COL14A1 SNPs (rs4870723, rs2305600, and rs2305598; P = 0.013, 0.019, and 0.028, respectively), a COL5A1 SNP (rs3827852; P = 0.016), and COL4A2 SNPs (rs76425569, rs388222, and rs2281968; P = 0.049 for the three, and rs445348, P = 0.040) and POP, respectively. Although there was no significant association between the COL3A1 SNP and POP, there was a trend toward significance for COL14A1 SNP (rs2305603), COL4A2 SNP (rs74941798), two COL1A1 SNPs (rs2586488 and rs2249492) and three COL18A1 SNPs (rs1050351, rs56335679, and rs55690336), and POP.

Conclusion:

We are the first to evaluate the relationship between COL14A1, COL5A1, and COL4A2 polymorphisms and POP, besides COL3A1, COL1A1, and COL18A1, which have been reported previously. We found several candidate SNPs that were significantly associated with prolapse in Chinese women. Our results provide new evidence for further investigation of the involvement of these potential genes in the etiology of POP.
Predicting Speech Outcomes After Cochlear Implantation in Older Adults Using the Self-administered Gerocognitive Examination Test
Authors: Wazen Jack J. , Kellermeyer Brian , Lange Linda , Rende Sharon , Ortega Carmelo , Rosenberg Seth
Published: October 2019

Purpose:

The purpose of this study is to determine if a cognitive test, Self-administered Gerocognitive Examination (SAGE), correlates with speech recognition outcomes 1 year after cochlear implantation in adults over 65 years of age.

Methods:

Retrospective study was conducted at a single institution. Surgery was performed by two surgeons on adult patients (>65 yrs) with postlingual bilateral sensorineural hearing loss meeting clinical and audiological candidacy for unilateral cochlear implantation. Patients who performed SAGE preimplantation, and speech testing (CNC, AzBio in quiet, AzBio in noise) before and 1 year after implantation were included.

Results:

Forty patients with a mean age of 78 were included. The overall mean preoperative SAGE score was 17.4 (95% CI 16.2–18.7). Greater than 17 is considered normal. Data demonstrated a statistically significant linear correlation between preoperative SAGE scores with change in speech testing 1 year postoperatively: CNC—Adjusted R-squared: 0.1955, p value: 0.002508; AzBio in quiet—Adjusted R-squared: 0.1564, p value: 0.006686; AzBio in noise—Adjusted R-squared: 0.1543, p value: 0.007053. Multivariate linear regression analysis revealed that age and SAGE scores both statistically correlated with speech testing 1 year after implantation (p = 0.01 for both). Patients who passed the SAGE (≥17) had statistically significant higher CNC, AzBio in quiet, and AzBio in noise scores 1 year postoperatively compared with patients with low SAGE scores (<17) despite statistically similar age means in each group.

Conclusion:

SAGE can predict speech recognition testing 1 year after cochlear implantation in older adults over 65 years of age.
Pollinator effectiveness and importance between female and male mining bee (Andrena)
Authors: Tang Ju , Quan Qiu-Mei , Chen Jing-Zhu , Wu Ting , Huang Shuang-Quan
Published: October 2019

Bees are often considered to be effective pollinators in both agricultural and natural ecosystems but could be ineffective pollinators in that they collect large quantities of pollen for food provision but deliver little to stigmas. Male bees do not collect pollen to feed larvae, and their pollination role has been underappreciated. Here we compare pollination effectiveness, visit frequency and pollen foraging behaviour between female and male individuals of a mining bee,Andrena emeishanica, visiting a nectariferous spring flower (Epimedium pubescens). Female bees were observed to forage for both pollen and nectar, but male bees foraged only for nectar. Female bees had large hairy hind tibiae with conspicuous scopae, and nearly 90% of the pollen grains they collected went onto the hind legs. Male bees removed less pollen from anthers than female bees but deposited more pollen on stigmas per visit. The higher pollen transfer efficiency of male bees was due to 48.4% of pollen grains remaining ungroomed on the thorax and abdomen, available for stigma contact, but their visitation rate to flowers was much lower. Our results indicate that male solitary bees could transfer more pollen on the stigmaper visitbut were less important (transferred less pollen in total, because they made fewer visits per unit time) than females.
Testing biodiversity theory using species richness of reef-building corals across a depth gradient
Authors: Roberts T. Edward , Keith Sally A. , Rahbek Carsten , Bridge Tom C. L. , Caley M. Julian , Baird Andrew H.
Published: October 2019

Natural environmental gradients encompass systematic variation in abiotic factors that can be exploited to test competing explanations of biodiversity patterns. The
species–energy
(SE) hypothesis attempts to explain species richness gradients as a function of energy availability. However, limited empirical support for SE is often attributed to idiosyncratic, local-scale processes distorting the underlying SE relationship. Meanwhile, studies are also often confounded by factors such as sampling biases, dispersal boundaries and unclear definitions of energy availability. Here, we used spatially structured observations of 8460 colonies of photo-symbiotic reef-building corals and a null-model to test whether energy can explain observed coral species richness over depth. Species richness was left-skewed, hump-shaped and unrelated to energy availability. While local-scale processes were evident, their influence on species richness was insufficient to reconcile observations with model predictions. Therefore, energy availability, either in isolation or in combination with local deterministic processes, was unable to explain coral species richness across depth. Our results demonstrate that local-scale processes do not necessarily explain deviations in species richness from theoretical models, and that the use of idiosyncratic small-scale factors to explain large-scale ecological patterns requires the utmost caution.
How moles walk; it's all thumbs
Authors: Lin Yi-Fen , Konow Nicolai , Dumont Elizabeth R.
Published: October 2019

A recurring theme in the evolution of tetrapods is the shift from sprawling posture with laterally orientated limbs to erect posture with the limbs extending below the body. However, in order to invade particular locomotor niches, some tetrapods secondarily evolved a sprawled posture. This includes moles, some of the most specialized digging tetrapods. Although their forelimb anatomy and posture facilitates burrowing, moles also walk long distances to forage for and transport food. Here, we use X-ray Reconstruction Of Moving Morphology (XROMM) to determine if the mole humerus rotates around its long axis during walking, as it does when moles burrow and echidnas walk, or alternatively protracts and retracts at the shoulder in the horizontal plane as seen in sprawling reptiles. Our results reject both hypotheses and demonstrate that forelimb kinematics during mole walking are unusual among those described for tetrapods. The humerus is retracted and protracted in the parasagittal plane above, rather than below the shoulder joint and the ‘false thumb’, a sesamoid bone (os falciforme), supports body weight during the stance phase, which is relatively short. Our findings broaden our understanding of the diversity of tetrapod limb posture and locomotor evolution, demonstrate the importance of X-ray-based techniques for revealing hidden kinematics and highlight the importance of examining locomotor function at the level of individual joint mobility.
Assessing the affective component of pain, and the efficacy of pain control, using conditioned place aversion in calves
Authors: Ede Thomas , von Keyserlingk Marina A. G. , Weary Daniel M.
Published: October 2019

Pain in animals is typically assessed using reflexive and physiological responses. These measures allow inferences regarding nociception but provide little basis for conclusions about the affective component of pain (i.e. how negatively the experience is perceived). Calves routinely undergo painful procedures on commercial farms, including hot-iron disbudding, providing a convenient model to study pain in animals. The aim of this study was to investigate the affective component of post-procedural pain due to hot-iron disbudding, using conditioned place aversion. Calves (n= 31) were subjected to two procedures (one bud at a time): one without post-procedural pain control and the other with the use of a nonsteroidal anti-inflammatory drug (either meloxicam (n= 16) or ketoprofen (n= 15)). All procedures included the use of local anaesthesia (lidocaine). Place conditioning was tested 2 days after the last treatment by allowing calves to freely roam between the pens where they had previously been disbudded. Calves spent more time, and lay down more frequently, in the pen where they received meloxicam compared with the pen where they only received a local block. Surprisingly, calves avoided the pen where they received ketoprofen compared with the control treatment pen. We hypothesize that the shorter duration of action of ketoprofen resulted in increasing pain at the end of the conditioning period, explaining the increased aversion to this treatment. These results illustrate the value of place conditioning paradigms to assess the affective component of pain in animals, and suggest that the animal's evaluation of painful events depends upon the time course of when the pain is experienced.
Three-dimensional functional gradients direct stem curling in the resurrection plant
Selaginella lepidophylla
Authors: Brulé Véronique , Rafsanjani Ahmad , Asgari Meisam , Western Tamara L. , Pasini Damiano
Published: October 2019

Upon hydration and dehydration, the vegetative tissue of
Selaginella lepidophylla
can reversibly swell and shrink to generate complex morphological transformations. Here, we investigate how structural and compositional properties at tissue and cell wall levels in
S. lepidophylla
lead to different stem curling profiles between inner and outer stems. Our results show that directional bending in both stem types is associated with cross-sectional gradients of tissue density, cell orientation and secondary cell wall composition between adaxial and abaxial stem sides. In inner stems, longitudinal gradients of cell wall thickness and composition affect tip-to-base tissue swelling and shrinking, allowing for more complex curling as compared to outer stems. Together, these features yield three-dimensional functional gradients that allow the plant to reproducibly deform in predetermined patterns that vary depending on the stem type. This study is the first to demonstrate functional gradients at different hierarchical levels combining to operate in a three-dimensional context.
Strong static magnetic field delayed the early development of zebrafish
Authors: Ge Shuchao , Li Jingchen , Huang Dengfeng , Cai Yuan , Fang Jun , Jiang Hongyuan , Hu Bing
Published: October 2019

One of the major topics in magnetobiology is the biological effects of strong static magnetic field (SMF) on living organisms. However, there has been a paucity of the comprehensive study of the long-term effects of strong SMF on an animal's development. Here, we explored this question with zebrafish, an excellent model organism for developmental study. In our research, zebrafish eggs, just after fertilization, were exposed to a 9.0 T SMF for 24 h, the critical period of post-fertilization development from cleavage to segmentation. The effects of strong SMF exposure on the following developmental progress of zebrafish were studied until 6 days post-fertilization (dpf). Results showed that 9.0 T SMF exposure did not influence the survival or the general developmental scenario of zebrafish embryos. However, it slowed down the developmental pace of the whole animal, and the late developers would catch up with their control peers after the SMF was removed. We proposed a mechanical model and deduced that the development delaying effect was caused by the interference of SMF in microtubule and spindle positioning during mitosis, especially in early cleavages. Our research data provide insights into how strong SMF influences the developing organisms through basic physical interactions with intracellular macromolecules.
Nucleotide excision repair genes shaping embryonic development
Authors: Araújo Sofia J. , Kuraoka Isao
Published: October 2019

Nucleotide excision repair (NER) is a highly conserved mechanism to remove helix-distorting DNA lesions. A major substrate for NER is DNA damage caused by environmental genotoxins, most notably ultraviolet radiation. Xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy are three human disorders caused by inherited defects in NER. The symptoms and severity of these diseases vary dramatically, ranging from profound developmental delay to cancer predisposition and accelerated ageing. All three syndromes include developmental abnormalities, indicating an important role for optimal transcription and for NER in protecting against spontaneous DNA damage during embryonic development. Here, we review the current knowledge on genes that function in NER that also affect embryonic development, in particular the development of a fully functional nervous system.
Functional identification of aStreptomyces lividansFKBP-like protein involved in the folding of overproduced secreted proteins
Authors: Vicente R. L. , Marín S. , Valverde J. R. , Palomino C. , Mellado R. P. , Gullón S.
Published: October 2019

Some bacterial peptidyl-prolylcis/transisomerases (PPIases) are involved in secretory protein folding after the translocation step.Streptomyces lividanshas been used as a host for engineering extracellular overproduction of homologous and heterologous proteins in industrial applications. Although the mechanisms governing the major secretory pathway (Sec route) and the minor secretory pathway (Tat route) are reasonably well described, the function of proteins responsible for the extracellular secretory protein folding is not characterized as yet. We have characterized a Tat-dependent S. lividansFK506-binding protein-like lipoprotein (FKBP) that has PPIase activity. A mutant in thesli-fkbpgene induces a secretion stress response and affects secretion and activity of the Sec-dependent protein α-amylase. Additionally, propagation in high copy number of thesli-fkbpgene has a positive effect on the activity of both the overproduced α-amylase and the overproduced Tat-dependent agarase, both containing prolinecisisomers. Targeted proteomic analyses showed that a relevant group of secreted proteins inS. lividansTK21 are affected by Sli-FKBP, revealing a wide substrate range. The results obtained indicate that, regardless of the secretory route used by proteins inS. lividans, adjusting the expression ofsli-fkbpmay facilitate folding of dependent proteins when engineeringStreptomycesstrains for the overproduction of homologous or heterologous secretory proteins.
Preserved collagen reveals species identity in archaeological marine turtle bones from Caribbean and Florida sites
Authors: Harvey Virginia L. , LeFebvre Michelle J. , deFrance Susan D. , Toftgaard Casper , Drosou Konstantina , Kitchener Andrew C. , Buckley Michael
Published: October 2019

Advancements in molecular science are continually improving our knowledge of marine turtle biology and evolution. However, there are still considerable gaps in our understanding, such as past marine turtle distributions, which can benefit from advanced zooarchaeological analyses. Here, we apply collagen fingerprinting to 130 archaeological marine turtle bone samples up to approximately 2500 years old from the Caribbean and Florida's Gulf Coast for faunal identification, finding the vast majority of samples (88%) to contain preserved collagen despite deposition in the tropics. All samples can be identified to species-level with the exception of the Kemp's ridley (
Lepidochelys kempii
) and olive ridley (
L. olivacea
) turtles, which can be separated to genus level, having diverged from one another only approximately 5 Ma. Additionally, we identify a single homologous peptide that allows the separation of archaeological green turtle samples,
Chelonia
spp., into two distinct groups, which potentially signifies a difference in genetic stock. The majority of the archaeological samples are identified as green turtle (
Chelonia
spp.; 63%), with hawksbill (
Eretmochelys imbricata
; 17%) and ridley turtles (
Lepidochelys
spp
.
; 3%) making up smaller proportions of the assemblage. There were no molecular identifications of the loggerhead turtle (
Caretta caretta
) in the assemblage despite 9% of the samples being morphologically identified as such, highlighting the difficulties in relying on morphological identifications alone in archaeological remains. Finally, we present the first marine turtle molecular phylogeny using collagen (I) amino acid sequences and find our analyses match recent phylogenies based on nuclear and mitochondrial DNA. Our results highlight the advantage of using collagen fingerprinting to supplement morphological analyses of turtle bones and support the usefulness of this technique for assessing their past distributions across the Caribbean and Florida's Gulf Coast, especially in these tropical environments where DNA preservation may be poor.
Gene drive for population genetic control: non-functional resistance and parental effects
Authors: Beaghton Andrea K. , Hammond Andrew , Nolan Tony , Crisanti Andrea , Burt Austin
Published: October 2019

Gene drive is a natural process of biased inheritance that, in principle, could be used to control pest and vector populations. As with any form of pest control, attention should be paid to the possibility of resistance evolving. For nuclease-based gene drive aimed at suppressing a population, resistance could arise by changes in the target sequence that maintain function, and various strategies have been proposed to reduce the likelihood that such alleles arise. Even if these strategies are successful, it is almost inevitable that alleles will arise at the target site that are resistant to the drive but do not restore function, and the impact of such sequences on the dynamics of control has been little studied. We use population genetic modelling of a strategy targeting a female fertility gene to demonstrate that such alleles may be expected to accumulate, and thereby reduce the reproductive load on the population, if nuclease expression
per se
causes substantial heterozygote fitness effects or if parental (especially paternal) deposition of nuclease either reduces offspring fitness or affects the genotype of their germline. All these phenomena have been observed in synthetic drive constructs. It will, therefore, be important to allow for non-functional resistance alleles in predicting the dynamics of constructs in cage populations and the impacts of any field release.
Burrowing detritivores regulate nutrient cycling in a desert ecosystem
Authors: Sagi Nevo , Grünzweig José M. , Hawlena Dror
Published: October 2019

Nutrient cycling in most terrestrial ecosystems is controlled by moisture-dependent decomposer activity. In arid ecosystems, plant litter cycling exceeds rates predicted based on precipitation amounts, suggesting that additional factors are involved. Attempts to reveal these factors have focused on abiotic degradation, soil–litter mixing and alternative moisture sources. Our aim was to explore an additional hypothesis that macro-detritivores control litter cycling in deserts. We quantified the role different organisms play in clearing plant detritus from the desert surface, using litter baskets with different mesh sizes that allow selective entry of micro-, meso- or macrofauna. We also measured soil nutrient concentrations in increasing distances from the burrows of a highly abundant macro-detritivore, the desert isopodHemilepistus reaumuri. Macro-detritivores controlled the clearing of plant litter in our field site. The highest rates of litter removal were measured during the hot and dry summer when isopod activity peaks and microbial activity is minimal. We also found substantial enrichment of inorganic nitrogen and phosphorous near isopod burrows. We conclude that burrowing macro-detritivores are important regulators of litter cycling in this arid ecosystem, providing a plausible general mechanism that explains the unexpectedly high rates of plant litter cycling in deserts.
Origin of horsetails and the role of whole-genome duplication in plant macroevolution
Authors: Clark James W. , Puttick Mark N. , Donoghue Philip C. J.
Published: October 2019

Whole-genome duplication (WGD) has occurred commonly in land plant evolution and it is often invoked as a causal agent in diversification, phenotypic and developmental innovation, as well as conferring extinction resistance. The ancient and iconic lineage of
Equisetum
is no exception, where WGD has been inferred to have occurred prior to the Cretaceous–Palaeogene (K–Pg) boundary, coincident with WGD events in angiosperms. In the absence of high species diversity, WGD in
Equisetum
is interpreted to have facilitated the long-term survival of the lineage. However, this characterization remains uncertain as these analyses of the
Equisetum
WGD event have not accounted for fossil diversity. Here, we analyse additional available transcriptomes and summarize the fossil record. Our results confirm support for at least one WGD event shared among the majority of extant
Equisetum
species. Furthermore, we use improved dating methods to constrain the age of gene duplication in geological time and identify two successive
Equisetum
WGD events. The two WGD events occurred during the Carboniferous and Triassic, respectively, rather than in association with the K–Pg boundary. WGD events are believed to drive high rates of trait evolution and innovations, but analysed trends of morphological evolution across the historical diversity of
Equisetum
provide little evidence for further macroevolutionary consequences following WGD. WGD events cannot have conferred extinction resistance to the
Equisetum
lineage through the K–Pg boundary since the ploidy events occurred hundreds of millions of years before this mass extinction and we find evidence of extinction among fossil polyploid
Equisetum
lineages. Our findings precipitate the need for a review of the proposed roles of WGDs in biological innovation and extinction survival in angiosperm and non-angiosperm lineages alike.
Serratia marcescens
shapes cutaneous bacterial communities and influences survival of an amphibian host
Authors: Madison Joseph D. , Ouellette Scot P. , Schmidt Emme L. , Kerby Jacob L.
Published: October 2019

Ongoing investigations into the interactions between microbial communities and their associated hosts are changing how emerging diseases are perceived and ameliorated. Of the numerous host–microbiome–disease systems of study, the emergence of chytridiomycosis (caused by
Batrachochytrium dendrobatidis
, hereafter
Bd
) has been implicated in ongoing declines and extinction events of amphibians worldwide. Interestingly, there has been differential survival among amphibians in resisting
Bd
infection and subsequent disease. One factor thought to contribute to this resistance is the host-associated cutaneous microbiota. This has raised the possibility of using genetically modified probiotics to restructure the host-associated microbiota for desired anti-fungal outcomes. Here, we use a previously described strain of
Serratia marcescens
(
Sm
) for the manipulation of amphibian cutaneous microbiota.
Sm
was genetically altered to have a dysfunctional pathway for the production of the extracellular metabolite prodigiosin. This genetically altered strain (Δ
pig
) and the functional prodigiosin producing strain (wild-type, WT) were compared for their microbial community and anti-
Bd
effects both
in vitro
and
in vivo
.
In vitro
,
Bd
growth was significantly repressed in the presence of prodigiosin.
In vivo
, the inoculation of both
Sm
strains was shown to significantly influence amphibian microbiota diversity with the Δ
pig-Sm
treatment showing increasing alpha diversity, and the WT-
Sm
having no temporal effect on diversity. Differences were also seen in host mortality with Δ
pig-Sm
treatments exhibiting significantly decreased survival probability when compared with WT-
Sm
in the presence of
Bd
. These results are an important proof-of-concept for linking the use of genetically modified probiotic bacteria to host microbial community structure and disease outcomes, which in the future may provide a way to ameliorate disease and address critical frontiers in disease and microbial ecology.
Simultaneous measurement of biochemical phenotypes and gene expression in single cells
Authors: Richer Amanda L. , Riemondy Kent A. , Hardie Lakotah , Hesselberth Jay R.
Published: October 2019

Methods to measure heterogeneity among cells are rapidly transforming our understanding of biology but are currently limited to molecular abundance measurements. We developed an approach to simultaneously measure biochemical activities and mRNA abundance in single cells to understand the heterogeneity of DNA repair activities across thousands of human lymphocytes, identifying known and novel cell-type-specific DNA repair phenotypes. Our approach provides a general framework for understanding functional heterogeneity among single cells.
Host-microbiome protein-protein interactions reveal mechanisms in human disease
Authors: Zhou Hao , Beltrán Juan Felipe , Brito Ilana Lauren
Published: October 2019

Host-microbe interactions are crucial for normal physiological and immune system development and are implicated in a wide variety of diseases, including inflammatory bowel disease (IBD), colorectal cancer (CRC), obesity, and type 2 diabetes (T2D). Despite large-scale case-control studies aimed at identifying microbial taxa or specific genes involved in pathogeneses, the mechanisms linking them to disease have thus far remained elusive. To identify potential mechanisms through which human-associated bacteria impact host health, we leveraged publicly-available interspecies protein-protein interaction (PPI) data to find clusters of microbiome-derived proteins with high sequence identity to known human protein interactors. We observe differential targeting of putative human-interacting bacterial genes in metagenomic case-control microbiome studies. In nine independent case studies, we find evidence that the microbiome broadly targets human proteins involved in immune, oncogenic, apoptotic, and endocrine signaling pathways in relation to IBD, CRC, obesity and T2D diagnoses. This host-centric analysis strategy provides a mechanistic hypothesis-generating platform for any metagenomics cohort study and extensively adds human functional annotation to commensal bacterial proteins.

One-sentence summary

Microbiome-derived proteins are linked to disease-associated human pathways by metagenomic and protein-protein interaction analyses.
Evaluating DCA-based method performances for RNA contact prediction by a well-curated dataset
Authors: Pucci F. , Zerihun M. , Peter E. , Schug A.
Published: October 2019

RNA molecules play many pivotal roles in the cellular functioning that are still not fully understood. Any detailed understanding of RNA function requires knowledge of its three-dimensional structure, yet experimental RNA structure resolution remains demanding. Recent advances in sequencing provide unprecedented amounts of sequence data that can be statistically analysed by methods such as Direct Coupling Analysis (DCA) to determine spatial proximity or contacts of specific nucleic acid pairs, which improve the quality of structure prediction. To quantify this structure prediction improvement, we here present a well curated dataset of about seventy RNA structures with high resolution and compare different nucleotide-nucleotide contact prediction methods available in the literature. We observe only minor difference between the performances of the different methods. Moreover, we discuss how these predictions are robust for different contact definitions and how strongly depend on procedures used to curate and align the families of homologous RNA sequences.
Sparse epistatic patterns in the evolution of terpene synthases
Authors: Ballal Aditya , Laurendon Caroline , Salmon Melissa , Vardakou Maria , Cheema Jitender , O’Maille Paul E. , Morozov Alexandre V.
Published: October 2019

We explore sequence determinants of enzyme activity and specificity in a major enzyme family of terpene synthases. Most enzymes in this family catalyze reactions that produce cyclic terpenes – complex hydrocarbons widely used by plants and insects in diverse biological processes such as defense, communication, and symbiosis. To analyze the molecular mechanisms of emergence of terpene cyclization, we have carried out in-depth examination of mutational space around (E)-β-farnesene synthase, an Artemisia annua enzyme which catalyzes production of a linear hydrocarbon chain. Each mutant enzyme in our synthetic libraries was characterized biochemically, and the resulting reaction rate data was used as input to the Michaelis-Menten model of enzyme kinetics, in which free energies were represented as sums of one-amino-acid contributions and two-amino-acid couplings. Our model predicts measured reaction rates with high accuracy and yields free energy landscapes characterized by relatively few coupling terms. As a result, the Michaelis-Menten free energy landscapes have simple, interpretable structure and exhibit little epistasis. We have also developed biophysical fitness models based on the assumption that highly fit enzymes have evolved to maximize the output of correct products, such as cyclic products or a specific product of interest, while minimizing the output of byproducts. This approach results in a non-linear fitness landscape which is considerably more epistatic. Overall, our experimental and computational framework provides focused characterization of evolutionary emergence of novel enzymatic functions in the context of micro-evolutionary exploration of sequence space around naturally occurring enzymes.