Miracle-dz/UniFAR-FTUs huggingface dataset:
Semiparametric modeling and estimation of heteroscedasticity in regression analysis of cross-sectional data

We consider the problem of modeling heteroscedasticity in semiparametric regression analysis of crosssectional data. Existing work in this setting is rather limited and mostly adopts a fully nonparametric variance structure. This approach is hampered by curse of dimensionality in practical applications. Moreover, the corresponding asymptotic theory is largely restricted to estimators that minimize certain smooth objective functions. The asymptotic derivation thus excludes semiparametric quantile regression models. To overcome these drawbacks, we study a general class of location-dispersion regression models, in which both the location function and the dispersion function are semiparametrically modeled. We establish uniﬁed asymptotic theory which is valid for many commonly used semiparametric structures such as the partially linear structure and single-index structure. We provide easy to check sufficient conditions and illustrate them through examples. Our theory permits non-smooth location or dispersion functions, thus allows for semiparametric quantile heteroscedastic regression and robust estimation in semiparametric mean regression. Simulation studies indicate significant efficiency gain in estimating the parametric component of the location function. The results are applied to analyzing a data set on gasoline consumption.
Purification and partial amino acid sequence of curvaticin FS47, a heat-stable bacteriocin produced by Lactobacillus curvatus FS47

Curvaticin FS47, a bacteriocin produced by Lactobacillus curvatus FS47, is inhibitory to Listeria monocytogenes, as well as Lactobacillus, Pediococcus, Enterococcus, and Bacillus spp. The bacteriocin was purified by 40% ammonium sulfate precipitation, solid-phase extraction, and reversed-phase high-pressure liquid chromatography. Purified curvaticin FS47 was determined to be 4.07 kDa by mass spectrometry and was partially sequenced. Thirty-one N-terminal amino acids were identified; the curvaticin FS47 protein sequence did not show homology to the pediocin-like group of bacteriocins.
Genome-Wide Binding Analysis of the Transcription Activator IDEAL PLANT ARCHITECTURE1 Reveals a Complex Network Regulating Rice Plant Architecture[W]

This work shows that the key rice architecture regulator IPA1 binds to promoters of target genes directly or indirectly at a different motif by interacting with PCF1 and PCF2. Expression profiling and further characterization of these target genes reveal a complex genetic regulatory network orchestrated by IPA1, providing insight into the regulation of plant development. IDEAL PLANT ARCHITECTURE1 (IPA1) is critical in regulating rice (Oryza sativa) plant architecture and substantially enhances grain yield. To elucidate its molecular basis, we first confirmed IPA1 as a functional transcription activator and then identified 1067 and 2185 genes associated with IPA1 binding sites in shoot apices and young panicles, respectively, through chromatin immunoprecipitation sequencing assays. The SQUAMOSA PROMOTER BINDING PROTEIN-box direct binding core motif GTAC was highly enriched in IPA1 binding peaks; interestingly, a previously uncharacterized indirect binding motif TGGGCC/T was found to be significantly enriched through the interaction of IPA1 with proliferating cell nuclear antigen PROMOTER BINDING FACTOR1 or PROMOTER BINDING FACTOR2. Genome-wide expression profiling by RNA sequencing revealed IPA1 roles in diverse pathways. Moreover, our results demonstrated that IPA1 could directly bind to the promoter of rice TEOSINTE BRANCHED1, a negative regulator of tiller bud outgrowth, to suppress rice tillering, and directly and positively regulate DENSE AND ERECT PANICLE1, an important gene regulating panicle architecture, to influence plant height and panicle length. The elucidation of target genes of IPA1 genome-wide will contribute to understanding the molecular mechanisms underlying plant architecture and to facilitating the breeding of elite varieties with ideal plant architecture.
Some predictors of psychiatric consultation in nursing home residents.

OBJECTIVE Despite the high rate of psychiatric disorders in nursing homes, research indicates that psychiatric consultation is requested infrequently. The authors sought to determine the rate of psychiatric consultation in a nursing home population and to assess what factors were related to a consultation request. METHODS Subjects were recruited from a stratified random sample of 59 nursing homes across Maryland. All new admissions age 65 years and older from September 1992 through March 1995 were eligible for the study. A total of 2,285 subjects were included in the study. Variables examined were factor scores from the Cornell Scale for Depression in Dementia and the Psychogeriatric Dependency Rating Scale (Behavioral Subscale), nursing home characteristics, and whether the resident had a psychiatric consultation within 90 days of admission. RESULTS Twenty percent of the residents (N=404) had a psychiatric consultation. There was no significant association with demographic variables. Behaviors that triggered a psychiatric consultation included agitation, physical/verbal abuse, wandering, and manic/destructive acts. A psychiatric consultation was also requested when residents displayed anxiety. Surprisingly, depression in retarded and psychotic residents did not trigger a psychiatric consult. CONCLUSION As expected, behavioral problems and agitation are common reasons for a psychiatric consultation. However, the resident who is depressed, particularly the quiet or retarded depressed resident, may be overlooked. In this context, it is important for the nursing staff to recognize that lethargy and social withdrawal may be signs of depression, and a referral to a psychiatrist may be in order.
Regulatory Forum Opinion Piece*

BACKGROUND Histopathology is one of the more subjective diagnostic tools used in human and veterinary medicine, and also one where levels of skill and experience can vary widely from one practitioner to another. This means that when this tool is transposed from its traditional application in disease diagnosis for individual patients to toxicology studies for safety evaluation of a drug or chemical for large populations, additional safeguards are warranted to ensure accuracy of the data and appropriate interpretation in the context of the study data as a whole. Although not a general regulatory requirement, in toxicology studies this is achieved through peer review. Typically, a second pathologist reviews the diagnoses and interpretations of the original study pathologist, with a consensus opinion being expressed in the pathology report. This minimizes the inherent subjectivity in diagnosis, and ensures that at least two practitioners concur on which of these agreed diagnoses are likely effects of treatment. In the context of pharmaceutical toxicology studies, primary histopathology evaluation is usually done by a pharmaceutical company (sponsor) pathologist or by a contract research organization (CRO) pathologist; peer review is most commonly performed by a sponsor company pathologist (although it may be done by another CRO pathologist). While the expectation is, of course, that the peer reviewer influences the final data and interpretation, regulators have expressed concern that there may be ‘‘undue influence’’ or ‘‘bias’’ from sponsors, such that retention of the pre–peer review data might be desirable. This issue formed the basis of a meeting between representatives of Pharmaceutical Research and Manufacturers of America (PhRMA) and Food and Drug Administration (FDA) in 2012, and also of a panel discussion among industry pathologists and regulators in Japan in 2009 (JSTP 2009). The proposed solution to these concerns is that the peer review process is made more transparent, as suggested recently in this journal (Englehardt et al. 2013) and directly by regulators within the last few months in a new draft OECD regulatory guidance that states:‘‘ . there is an expectation that the initial review of the pathology data will have been completed before the peer review takes place and if changes are required, these are clearly documented and explained in the final report. ’’ Although documentation of the peer review process would indeed provide some additional transparency to data changes made following peer review, it is my opinion that need for this additional documentation has not been adequately demonstrated, the benefits are doubtful, and it also has significant drawbacks that could have a net negative impact on the quality of data provided for human risk assessment.
Inertial response from remote offshore wind farms connected through VSC-HVDC links: A Communication-less scheme

A communication-less scheme that allows remote offshore wind farms connected through HVDC links to participate in primary frequency control and contribute to system inertia is discussed in this paper. As a HVDC link decouples the offshore system from the onshore side, real-time communication of onshore frequency is normally required for the primary frequency control loop of the wind farms. Dependance on remote communication which could be unreliable at times is a problem. To obviate the need for communication, appropriate droop control on the offshore and onshore converters is used in this paper to translate the variation in onshore frequency to an equivalent variation on the offshore end. Thus the need for communicating onshore frequency to the offshore side is mitigated which ensures reliable operation. Such a communication-less scheme is compared against the conventional approach involving remote communication of onshore grid frequency to the wind farm site. Along side physical and analytical justification, a case study is presented to demonstrate that the communication-less scheme performs similar to the conventional one in terms of reducing grid frequency variations.
The Arguments and Data in Favor of Minimum Grading.

The arguments and for and against minimum grading systems have grown increasingly more intense and acrimonious in the past decade. However, there has been an absence of empirical data, theory and clear comparative analyses of conflicting points of view. Critics of minimum grading contend that the practice will produce grade inflation and social promotions of those students receiving minimum grades as the two chief arguments against minimum grading practices. In our retrospective study, we found no evidence of grade inflation or social promotion of those students receiving minimum grades in a large urban High School using a school-wide macro minimum grading system over a sevenyear period. We also found most of the benefits posited by minimum grading theory, including students who received minimum grades doing significantly better on state exams than would be predicted by the overall GPA’s with the opposite results being true for the other students in this High School. The far-reaching implications of these results for educators looking to implement fairer and more accurate student assessment are discussed here, including the documented benefits of minimum grading as sound educational and grading policy, and the need of a minimum-grading component in any sound grading system.
STRESS – THE RISK FACTOR IN THE LIP AND PALATE CLEFT DEVELOPMENT

Lip and palate cleft (cheilognathopalatoschisis) is most often congenital defect that affects craniofacial region. It is characterized by a difficult clinical presentation. The etiology is multicausal and not yet fully understood. The examination of numerous etiological factors imposed the need to study the role of stress in the development of lip and palate cleft. This is all the more important for the socioeconomic factors that characterized our society in the last years, after bombardment, poverty, higher divorce rate, and more family violence. The aim of this paper was to establish the importance of stressful events and their role in the development of lip and palate cleft. The examination included children born from March 1999 (time of war in this area), till December 2003, as well as their mothers. The study group comprised 96 children with the lip and palate cleft anomaly, and the control one included 142 healthy children. The chosen examinees were not under the influence of other etiological factors, such as heritage. The examination was conducted using a questionnaire containing questions related to stressful situations in the first trimester of pregnancy. The questions were thus formed so as to be clear to mothers of different levels of education, without expert phrases, except in the cases where it was necessary. The statistical differences between the study and control group were determined using Pearson's χ test. In the first trimester, the mothers of the study group, in regard to the control group, statistically more often had fears or anxiety (p<0.01), disorganized emotional life (p<0.001), more often phychological harassment (p<0.001), and the presence of any kind of harassment (p<0.001). The presence of stress was also greater in the study group, on the significance borderline in relation to the control group. The stressful situations to which mothers of the study group were exposed are in correlation with the increase of the children with lip and palate cleft. Acta Medica Medianae 2007;46(4):15-19.
Detailed staging of inbred C57BL/6 mice between Theiler's [1972] stages 18 and 21 (11-13 days of gestation) based on craniofacial development.

A detailed staging table of inbred C57BL/6 embryonic mice was developed to facilitate a study of the stage-by-stage cellular and molecular mechanisms underlying cranial skeletal development and elucidation of the developmental mechanisms potentially involved in evolutionary changes in cranial skeletal morphology exhibited by different inbred strains of mice. Mice were mated for only 2 hr and embryos were recovered every 2 or 4 hr between 11 and 13 days of gestation. Theiler's [1972] stages 18 through 21 were divided into substages and divisions based on the development of five external structures--the frontonasal area, eyes, auditory meatus, mandibular and hyoid auricular hillocks/pinna, and vibrissae--and three internal histological structures--eyes, tongue, and vibrissae. Each substage and division was designated with a decimal point: e.g., substage 20.1 and division 20.11. Embryos were staged using the staging table and the relationship of the substages and divisions with days of gestation was examined. The results showed considerable intra- and inter-litter variation in stages of embryos, suggesting that days of gestation are not a good indicator for staging embryos. Our staging table offers a more reliable and precise method to standardize embryonic development. Regression analyses of substages on days of gestation showed that the duration of stages increased from stages 18 to 21. Estimated durations were 3.5 hr for stages 18 and 19, 8.8 hr for stage 20, and 38.8 hr for stage 21. Our staging table also provides baseline information on development of the frontonasal area (muzzle) and vibrissae and development and the transformation of the auricular hillocks into the pinna. The developmental sequence of mystacial and labial vibrissae indicated highly regulated differentiation and morphogenesis of vibrissal development at stages 20 and 21. Three hyoid auricular hillocks transiently became four hillocks at stage 19.1 before transforming to the pinna during stage 21. The second and third hyoid auricular hillocks were the major contributor to the pinna before stage 21.2, whereas mandibular auricular hillocks contributed to the pinna from stage 21.32 onward. The staging table has already served to demonstrate stage-specific skeletogenesis of the first arch cartilages in inbred C57BL/6 mice and to reveal differences in the onset of timing of skeletogenesis among inbred C57BL/6, C3H/He and CBA/J mice.
Blended Rule-Based Energy Management for PHEV: System Structure and Strategy

This paper proposes a blended rule-based energy management system (EMS) for a plug-in hybrid electric vehicle (PHEV). The proposed EMS is formulated over driving information and vehicle trip energy and not over vehicle speed profiles, as usually seen. The proposed EMS design structure and strategy is described followed by its evaluation. This is the first time a platform for a rule-based acausal EMS has been designed. Performance metrics such as the fuel economy and the number of engine stop-starts are compared with conventional rule-based EMS over real-world destinations with uncertain trip demand. Its performance metrics compared with a conventional EMS for a full parallel PHEV was found to be superior in this paper.
Low‐Dose Irinotecan Improves Advanced Lupus Nephritis in Mice Potentially by Changing DNA Relaxation and Anti–Double‐Stranded DNA Binding

Despite clear advances in the treatment of systemic lupus erythematosus (SLE), many patients still present with refractory lupus nephritis, requiring new treatment strategies for this disease. This study was undertaken to determine whether reduced doses of the topoisomerase I (topo I) inhibitor irinotecan, which is known as a chemotherapeutic agent, suppress SLE in (NZB × NZW)F1 (NZB/NZW) mice, and to evaluate the potential mechanism by which irinotecan influences the course of SLE.
Public Trading and Private Incentives

This paper studies the link between public trading and the activity of a firm's large shareholder who can affect firm value. Public trading results in the formation of a stock price that is informative about the large shareholder's activity. This increases the latter's incentives to engage in value increasing activities. Indeed, if he has to liquidate part of his stake before the effect of his activity is publicly observed, a more informative price rewards him for his activity. Implications of this perspective are derived for the decision to go public and security design.
The Effects of Clopidogrel (Plavix) and Other Oral Anticoagulants on Early Hip Fracture Surgery

Objective: Risk for bleeding complications during and after early hip fracture surgery for patients taking clopidogrel and other anticoagulants have not been defined. The purpose of this study is to assess the perioperative bleeding risks and clinical outcome after early hip fracture surgery performed on patients taking clopidogrel (Plavix) and other oral anticoagulants. Design: Study design is a retrospective cohort analysis using data extracted from hospital records and state death records. Setting: Regional medical center (level II trauma). Methods: Data for 1118 patients ≥60 years of age who had surgical treatment for a hip fracture between 2004 and 2008 were reviewed. Eighty-two patients undergoing late surgery (>3 days after admission) were excluded. Patients taking clopidogrel were compared against those not taking clopidogrel. In addition, patients taking clopidogrel only were compared against cohorts of patients taking both clopidogrel and aspirin, aspirin only, warfarin only, or no anticoagulant. Results: Seventy-four of 1036 patients (7%) were taking clopidogrel, although control groups included 253 patients on aspirin alone, 90 patients on warfarin, and 619 taking no anticoagulants. No significant differences were noted between patients taking clopidogrel and those not taking clopidogrel in estimated blood loss, transfusion requirement, final blood count, hematoma evacuation, hospital length of stay (LOS), or mortality while in hospital or at 1 year. A higher American Society of Anesthesiologists score was seen in the clopidogrel and warfarin groups (P = 0.05 each), increased LOS in the clopidogrel group (P = 0.05), and higher rate of deep vein thrombosis seen in those patients taking warfarin (P = 0.05). Clopidogrel only versus aspirin versus both aspirin and clopidogrel, versus no anticoagulant versus warfarin showed no significant differences in estimated blood loss, transfusion requirement, final blood count, bleeding or perioperative complications, or mortality. Conclusions: Patients undergoing early hip fracture surgery who are taking clopidogrel, aspirin, or warfarin (with regulated international normalized ratio) are not at substantially increased risk for bleeding, bleeding complications, or mortality. Comorbidities and American Society of Anesthesiologists scores were significantly higher in the clopidogrel group, which may have resulted in the increased postoperative LOS in this group. Level of Evidence: Prognostic Level II. See Instructions for Authors for a complete description of levels of evidence.
Ultrastructural Localization of the Herpes Simplex Virus Type 1 UL31, UL34, and US3 Proteins Suggests Specific Roles in Primary Envelopment and Egress of Nucleocapsids

ABSTRACT The wild-type UL31, UL34, and US3 proteins localized on nuclear membranes and perinuclear virions; the US3 protein was also on cytoplasmic membranes and extranuclear virions. The UL31 and UL34 proteins were not detected in extracellular virions. US3 deletion caused (i) virion accumulation in nuclear membrane invaginations, (ii) delayed virus production onset, and (iii) reduced peak virus titers. These data support the herpes simplex virus type 1 deenvelopment-reenvelopment model of virion egress and suggest that the US3 protein plays an important, but nonessential, role in the egress pathway.
Sweet to the extreme: protein glycosylation in Archaea

Post‐translational modifications account for much of the biological diversity generated at the proteome level. Of these, glycosylation is the most prevalent. Long thought to be unique to Eukarya, it is now clear that both Bacteria and Archaea are also capable of N‐glycosylation, namely the covalent linkage of oligosaccharides to select target asparagine residues. However, while the eukaryal and bacterial N‐glycosylation pathways are relatively well defined, little is known of the parallel process in Archaea. Of late, however, major advances have been made in describing the process of archaeal N‐glycosylation. Such efforts have shown, as is often the case in archaeal biology, that protein N‐glycosylation in Archaea combines particular aspects of the eukaryal and bacterial pathways along with traits unique to this life form. For instance, while the oligosaccharides of archaeal glycoproteins include nucleotide‐activated sugars formed by bacterial pathways, the lipid carrier on which such oligosaccharides are assembled is the same as used in eukaryal N‐glycosylation. By contrast, transfer of assembled oligosaccharides to their protein targets shows Archaea‐specific properties. Finally, addressing N‐glycosylation from an archaeal perspective is providing new general insight into this event, as exemplified by the solution of the first crystal structure of an oligosaccharide transferase from an archaeal source.